diff --git a/.pylintrc b/.pylintrc index 5b77e41e8..73b83b4f4 100644 --- a/.pylintrc +++ b/.pylintrc @@ -18,7 +18,12 @@ ignore-patterns= #init-hook= # Use multiple processes to speed up Pylint. -jobs=1 +jobs=2 + +# Control the amount of potential inferred values when inferring a single +# object. This can help the performance when dealing with large functions or +# complex, nested conditions. +limit-inference-results=100 # List of plugins (as comma separated values of python modules names) to load, # usually to register additional checkers. @@ -54,92 +59,20 @@ confidence= # --enable=similarities". If you want to run only the classes checker, but have # no Warning level messages displayed, use"--disable=all --enable=classes # --disable=W" -disable=print-statement, - parameter-unpacking, - unpacking-in-except, - old-raise-syntax, - backtick, - long-suffix, - old-ne-operator, - old-octal-literal, - import-star-module-level, - non-ascii-bytes-literal, - raw-checker-failed, - bad-inline-option, - locally-disabled, - locally-enabled, - file-ignored, - suppressed-message, - useless-suppression, - deprecated-pragma, - apply-builtin, - basestring-builtin, - buffer-builtin, - cmp-builtin, - coerce-builtin, - execfile-builtin, - file-builtin, - long-builtin, - raw_input-builtin, - reduce-builtin, - standarderror-builtin, - unicode-builtin, - xrange-builtin, - coerce-method, - delslice-method, - getslice-method, - setslice-method, - no-absolute-import, - old-division, - dict-iter-method, - dict-view-method, - next-method-called, - metaclass-assignment, - indexing-exception, - raising-string, - reload-builtin, - oct-method, - hex-method, - nonzero-method, - cmp-method, - input-builtin, - round-builtin, - intern-builtin, - unichr-builtin, - map-builtin-not-iterating, - zip-builtin-not-iterating, - range-builtin-not-iterating, - filter-builtin-not-iterating, - using-cmp-argument, - eq-without-hash, - div-method, - idiv-method, - rdiv-method, - exception-message-attribute, - invalid-str-codec, - sys-max-int, - bad-python3-import, - deprecated-string-function, - deprecated-str-translate-call, - deprecated-itertools-function, - deprecated-types-field, - next-method-defined, - dict-items-not-iterating, - dict-keys-not-iterating, - dict-values-not-iterating, +disable=too-few-public-methods, + missing-docstring, + logging-not-lazy, + logging-fstring-interpolation, + logging-format-interpolation, + import-error, missing-docstring, abstract-method, - bad-continuation, - logging-format-interpolation, invalid-name, - bad-whitespace, - wrong-import-order, too-few-public-methods, keyword-arg-before-vararg, arguments-differ, - line-too-long, - import-error, - no-self-use + attribute-defined-outside-init, + relative-beyond-top-level # Enable the message, report, category or checker with the given id(s). You can # either give multiple identifier separated by comma (,) or put this option @@ -178,6 +111,11 @@ score=yes # Maximum number of nested blocks for function / method body max-nested-blocks=5 +# Complete name of functions that never returns. When checking for +# inconsistent-return-statements if a never returning function is called then +# it will be considered as an explicit return statement and no message will be +# printed. +never-returning-functions=sys.exit [BASIC] @@ -329,6 +267,10 @@ single-line-if-stmt=no # function parameter format logging-modules=logging +# Format style used to check logging format string. `old` means using % +# formatting, while `new` is for `{}` formatting. +logging-format-style=new + [MISCELLANEOUS] @@ -373,6 +315,14 @@ spelling-private-dict-file= spelling-store-unknown-words=no +[STRING] + +# This flag controls whether the implicit-str-concat-in-sequence should +# generate a warning on implicit string concatenation in sequences defined over +# several lines. +check-str-concat-over-line-jumps=no + + [TYPECHECK] # List of decorators that produce context managers, such as @@ -389,6 +339,10 @@ generated-members= # mixin class is detected if its name ends with "mixin" (case insensitive). ignore-mixin-members=yes +# Tells whether to warn about missing members when the owner of the attribute +# is inferred to be None. +ignore-none=yes + # This flag controls whether pylint should warn about no-member and similar # checks whenever an opaque object is returned when inferring. The inference # can return multiple potential results while evaluating a Python object, but @@ -470,7 +424,7 @@ exclude-protected=_asdict, valid-classmethod-first-arg=cls # List of valid names for the first argument in a metaclass class method. -valid-metaclass-classmethod-first-arg=mcs +valid-metaclass-classmethod-first-arg=cls [DESIGN] @@ -542,5 +496,6 @@ known-third-party=enchant [EXCEPTIONS] # Exceptions that will emit a warning when being caught. Defaults to -# "Exception" -overgeneral-exceptions=Exception +# "BaseException, Exception". +overgeneral-exceptions=BaseException, + Exception diff --git a/.travis.yml b/.travis.yml index df42263ba..4595cbe93 100644 --- a/.travis.yml +++ b/.travis.yml @@ -12,7 +12,9 @@ before_install: install: - pip install -r backend/requirements.txt - pip install -r test/requirements.txt + - pip install -r scripts/importer/requirements.txt - pip install coverage coveralls + - pip install pylint script: - test/travis_script.sh addons: diff --git a/backend/application.py b/backend/application.py index 5641c31a4..d5ffde0da 100644 --- a/backend/application.py +++ b/backend/application.py @@ -1,50 +1,50 @@ +from datetime import datetime, timedelta from email.mime.multipart import MIMEMultipart from email.mime.text import MIMEText -from os import path import logging -from datetime import datetime, timedelta -from peewee import fn -import peewee +import math +from os import path +import re +import random import smtplib import socket -import tornado.web -import tornado -import random import string import uuid -import math -import re + +from peewee import fn +import peewee +import tornado.web +import tornado import db import handlers import settings from modules.browser import utils - def build_dataset_structure(dataset_version, user=None, dataset=None): if dataset is None: dataset = dataset_version.dataset - r = db.build_dict_from_row(dataset) + row = db.build_dict_from_row(dataset) - r['version'] = db.build_dict_from_row(dataset_version) - r['version']['available_from'] = r['version']['available_from'].strftime('%Y-%m-%d') + row['version'] = db.build_dict_from_row(dataset_version) + row['version']['available_from'] = row['version']['available_from'].strftime('%Y-%m-%d') - r['has_image'] = dataset.has_image() + row['has_image'] = dataset.has_image() if user: - r['is_admin'] = user.is_admin(dataset) + row['is_admin'] = user.is_admin(dataset) if user.has_access(dataset, dataset_version.version): - r['authorization_level'] = 'has_access' + row['authorization_level'] = 'has_access' elif user.has_requested_access(dataset): - r['authorization_level'] = 'has_requested_access' + row['authorization_level'] = 'has_requested_access' else: - r['authorization_level'] = 'no_access' + row['authorization_level'] = 'no_access' - return r + return row class QuitHandler(handlers.UnsafeHandler): - def get(self): + def get(self): # pylint: disable=no-self-use ioloop = tornado.ioloop.IOLoop.instance() ioloop.stop() @@ -65,7 +65,7 @@ def get(self): version = None beacon = None try: - url = self.get_argument('url') + url = self.get_argument('url') # pylint: disable=no-value-for-parameter match = re.match(".*/dataset/([^/]+)(/version/([^/]+))?", url) if match: dataset = match.group(1) @@ -77,14 +77,17 @@ def get(self): base = {"@context": "http://schema.org/", "@type": "DataCatalog", "name": "SweFreq", - "alternateName": [ "The Swedish Frequency resource for genomics" ], - "description": "The Swedish Frequency resource for genomics (SweFreq) is a website developed to make genomic datasets more findable and accessible in order to promote collaboration, new research and increase public benefit.", + "alternateName": ["The Swedish Frequency resource for genomics"], + "description": ("The Swedish Frequency resource for genomics (SweFreq) is a " + + "website developed to make genomic datasets more findable and " + + "accessible in order to promote collaboration, new research and " + + "increase public benefit."), "url": "https://swefreq.nbis.se/", "provider": { "@type": "Organization", "name": "National Bioinformatics Infrastructure Sweden", - "alternateName": [ "NBIS", - "ELIXIR Sweden" ], + "alternateName": ["NBIS", + "ELIXIR Sweden"], "logo": "http://nbis.se/assets/img/logos/nbislogo-green.svg", "url": "https://nbis.se/" }, @@ -94,43 +97,37 @@ def get(self): "@type": "CreativeWork", "name": "GNU General Public License v3.0", "url": "https://www.gnu.org/licenses/gpl-3.0.en.html" - } - } + }} if dataset: - dataset_schema = {'@type':"Dataset"} - - try: - dataset_version = db.get_dataset_version(dataset, version) - if dataset_version is None: - self.send_error(status_code=404) + dataset_schema = {'@type': "Dataset"} + + dataset_version = db.get_dataset_version(dataset, version) + if dataset_version is None: + self.send_error(status_code=404) + return + + if dataset_version.available_from > datetime.now(): + # If it's not available yet, only return if user is admin. + if not (self.current_user and + self.current_user.is_admin(dataset_version.dataset)): + self.send_error(status_code=403) return + base_url = "%s://%s" % (self.request.protocol, self.request.host) + dataset_schema['url'] = base_url + "/dataset/" + dataset_version.dataset.short_name + dataset_schema['@id'] = dataset_schema['url'] + dataset_schema['name'] = dataset_version.dataset.short_name + dataset_schema['description'] = dataset_version.description + dataset_schema['identifier'] = dataset_schema['name'] + dataset_schema['citation'] = dataset_version.ref_doi - if dataset_version.available_from > datetime.now(): - # If it's not available yet, only return if user is admin. - if not (self.current_user and self.current_user.is_admin(dataset_version.dataset)): - self.send_error(status_code=403) - return - - base_url = "%s://%s" % (self.request.protocol, self.request.host) - dataset_schema['url'] = base_url + "/dataset/" + dataset_version.dataset.short_name - dataset_schema['@id'] = dataset_schema['url'] - dataset_schema['name'] = dataset_version.dataset.short_name - dataset_schema['description'] = dataset_version.description - dataset_schema['identifier'] = dataset_schema['name'] - dataset_schema['citation'] = dataset_version.ref_doi - - base["dataset"] = dataset_schema - - except db.DatasetVersion.DoesNotExist as e: - logging.error("Dataset version does not exist: {}".format(e)) - except db.DatasetVersionCurrent.DoesNotExist as e: - logging.error("Dataset does not exist: {}".format(e)) + base["dataset"] = dataset_schema if beacon: base = {"@context": "http://schema.org", - "@id": "https://swefreq.nbis.se/api/beacon-elixir/", # or maybe "se.nbis.swefreq" as in the beacon api? + # or maybe "se.nbis.swefreq" as in the beacon api? + "@id": "https://swefreq.nbis.se/api/beacon-elixir/", "@type": "Beacon", "dataset": [dataset_schema], "dct:conformsTo": "https://bioschemas.org/specifications/drafts/Beacon/", @@ -140,8 +137,7 @@ def get(self): "description": "Beacon API Web Server based on the GA4GH Beacon API", "version": "1.1.0", # beacon api version "aggregator": False, - "url": "https://swefreq.nbis.se/api/beacon-elixir/" - } + "url": "https://swefreq.nbis.se/api/beacon-elixir/"} self.finish(base) @@ -160,17 +156,17 @@ def get(self): .where(db.DatasetVersion.available_from > datetime.now(), db.DatasetAccess.user == user, db.DatasetAccess.is_admin)) - for f in futures: - dataset = build_dataset_structure(f, user) + for fut in futures: + dataset = build_dataset_structure(fut, user) dataset['future'] = True - ret.append( dataset ) + ret.append(dataset) for version in db.DatasetVersionCurrent.select(): dataset = build_dataset_structure(version, user) dataset['current'] = True - ret.append( dataset ) + ret.append(dataset) - self.finish({'data':ret}) + self.finish({'data': ret}) class GetDataset(handlers.UnsafeHandler): @@ -208,27 +204,25 @@ def get(self, dataset): data = [] found_current = False versions = sorted(versions, key=lambda version: version.version) - for v in reversed(versions): + for ver in reversed(versions): current = False - future = False + future = False # Skip future versions unless admin - if v.available_from > datetime.now(): + if ver.available_from > datetime.now(): if not (user and user.is_admin(dataset)): continue future = True # Figure out if this is the current version - if not found_current and v.available_from < datetime.now(): + if not found_current and ver.available_from < datetime.now(): found_current = True - current = True + current = True - data.insert(0, { - 'name': v.version, - 'available_from': v.available_from.strftime('%Y-%m-%d'), - 'current': current, - 'future': future, - }) + data.insert(0, {'name': ver.version, + 'available_from': ver.available_from.strftime('%Y-%m-%d'), + 'current': current, + 'future': future}) self.finish({'data': data}) @@ -242,25 +236,20 @@ def post(self, dataset, ds_version=None): self.send_error(status_code=404) return - lh = db.Linkhash.create( - user = user, - dataset_version = dataset_version, - hash = uuid.uuid4().hex, - expires_on = datetime.now() + timedelta(hours=3), - ) + link_hash = db.Linkhash.create(user=user, + dataset_version=dataset_version, + hash=uuid.uuid4().hex, + expires_on=datetime.now() + timedelta(hours=3)) try: (db.Linkhash.delete() - .where(db.Linkhash.expires_on < datetime.now()) - .execute() - ) - except peewee.OperationalError as e: - logging.error("Could not clean old linkhashes: {}".format(e)) + .where(db.Linkhash.expires_on < datetime.now()) + .execute()) + except peewee.OperationalError as err: + logging.error(f"Could not clean old linkhashes: {err}") - self.finish({ - 'hash': lh.hash, - 'expires_on': lh.expires_on.strftime("%Y-%m-%d %H:%M") #pylint: disable=no-member - }) + self.finish({'hash': link_hash.hash, + 'expires_on': link_hash.expires_on.strftime("%Y-%m-%d %H:%M")}) # pylint: disable=no-member class DatasetFiles(handlers.AuthorizedHandler): @@ -272,23 +261,24 @@ def get(self, dataset, ds_version=None): return ret = [] - for f in dataset_version.files: - d = db.build_dict_from_row(f) - d['dirname'] = path.dirname(d['uri']) - d['human_size'] = format_bytes(d['file_size']) - ret.append(d) + for dv_file in dataset_version.files: + file_dict = db.build_dict_from_row(dv_file) + file_dict['dirname'] = path.dirname(file_dict['uri']) + file_dict['human_size'] = format_bytes(file_dict['file_size']) + ret.append(file_dict) self.finish({'files': ret}) def format_bytes(nbytes): postfixes = ['b', 'Kb', 'Mb', 'Gb', 'Tb', 'Pb', 'Eb'] - exponent = math.floor( math.log(nbytes) / math.log(1000) ) - return "{} {}".format( round(nbytes/1000**exponent, 2), postfixes[exponent]) + exponent = math.floor(math.log(nbytes) / math.log(1000)) + return f"{round(nbytes/1000**exponent, 2)} {postfixes[exponent]}" class Collection(handlers.UnsafeHandler): def get(self, dataset, ds_version=None): + del ds_version dataset, _ = utils.parse_dataset(dataset) dataset = db.get_dataset(dataset) @@ -296,17 +286,14 @@ def get(self, dataset, ds_version=None): for sample_set in dataset.sample_sets: collection = sample_set.collection - if not collection.name in collections: - collections[collection.name] = { - 'sample_sets': [], - 'ethnicity': collection.ethnicity, - } - collections[collection.name]['sample_sets'].append( db.build_dict_from_row(sample_set) ) - + if collection.name not in collections: + collections[collection.name] = {'sample_sets': [], + 'ethnicity': collection.ethnicity} + collections[collection.name]['sample_sets'].append(db.build_dict_from_row(sample_set)) ret = { 'collections': collections, - 'study': db.build_dict_from_row(dataset.study) + 'study': db.build_dict_from_row(dataset.study) } ret['study']['publication_date'] = ret['study']['publication_date'].strftime('%Y-%m-%d') @@ -317,14 +304,12 @@ class GetUser(handlers.UnsafeHandler): def get(self): user = self.current_user - ret = { 'user': None, 'email': None, 'login_type': 'none' } + ret = {'user': None, 'email': None, 'login_type': 'none'} if user: - ret = { - 'user': user.name, - 'email': user.email, - 'affiliation': user.affiliation, - 'country': user.country, - } + ret = {'user': user.name, + 'email': user.email, + 'affiliation': user.affiliation, + 'country': user.country} self.finish(ret) @@ -388,40 +373,36 @@ def country_list(self): "Uganda", "Ukraine", "United Arab Emirates", "United Kingdom", "United States", "Uruguay", "Uzbekistan", "Vanuatu", "Vatican", "Venezuela", "Vietnam", "Wallis and Futuna", "Western Sahara", - "Yemen", "Zambia", "Zimbabwe" ] + "Yemen", "Zambia", "Zimbabwe"] class RequestAccess(handlers.SafeHandler): def post(self, dataset): dataset, _ = utils.parse_dataset(dataset) - user = self.current_user + user = self.current_user dataset = db.get_dataset(dataset) - affiliation = self.get_argument("affiliation", strip=False) - country = self.get_argument("country", strip=False) - newsletter = self.get_argument("newsletter", strip=False) + affiliation = self.get_argument("affiliation", strip=False) # pylint: disable=no-value-for-parameter + country = self.get_argument("country", strip=False) # pylint: disable=no-value-for-parameter + newsletter = self.get_argument("newsletter", strip=False) # pylint: disable=no-value-for-parameter user.affiliation = affiliation user.country = country - logging.info("Inserting into database: {}, {}".format(user.name, user.email)) + logging.info(f"Inserting into database: {user.name}, {user.email}") try: with db.database.atomic(): - user.save() # Save to database - (da,_) = db.DatasetAccess.get_or_create( - user = user, - dataset = dataset - ) - da.wants_newsletter = newsletter - da.save() - db.UserAccessLog.create( - user = user, - dataset = dataset, - action = 'access_requested' - ) - except peewee.OperationalError as e: - logging.error("Database Error: {}".format(e)) + user.save() # Save to database + ds_access, _ = db.DatasetAccess.get_or_create(user=user, + dataset=dataset) + ds_access.wants_newsletter = newsletter + ds_access.save() + db.UserAccessLog.create(user=user, + dataset=dataset, + action='access_requested') + except peewee.OperationalError as err: + logging.error(f"Database Error: {err}") class LogEvent(handlers.SafeHandler): @@ -431,17 +412,14 @@ def post(self, dataset, event, target): if event == 'consent': user.save() - dv = (db.DatasetVersion - .select() - .join(db.Dataset) - .where( - db.DatasetVersion.version == target, - db.Dataset.short_name == dataset) - .get()) - db.UserConsentLog.create( - user = user, - dataset_version = dv, - ) + ds_version = (db.DatasetVersion + .select() + .join(db.Dataset) + .where(db.DatasetVersion.version == target, + db.Dataset.short_name == dataset) + .get()) + db.UserConsentLog.create(user=user, + dataset_version=ds_version) else: raise tornado.web.HTTPError(400, reason="Can't log that") @@ -454,74 +432,69 @@ def post(self, dataset, email): user = db.User.select().where(db.User.email == email).get() - da = db.DatasetAccess.select().where( - db.DatasetAccess.user == user, - db.DatasetAccess.dataset == dataset - ).get() - da.has_access = True - da.save() + ds_access = (db.DatasetAccess.select() + .where(db.DatasetAccess.user == user, + db.DatasetAccess.dataset == dataset) + .get()) + ds_access.has_access = True + ds_access.save() - db.UserAccessLog.create( - user = user, - dataset = dataset, - action = 'access_granted' - ) + db.UserAccessLog.create(user=user, + dataset=dataset, + action='access_granted') try: msg = MIMEMultipart() msg['to'] = email - msg['from'] = settings.from_address + msg['from'] = settings.from_address # pylint: disable=no-member msg['subject'] = 'Swefreq access granted to {}'.format(dataset.short_name) - msg.add_header('reply-to', settings.reply_to_address) + msg.add_header('reply-to', settings.reply_to_address) # pylint: disable=no-member body = """You now have access to the {} dataset Please visit https://swefreq.nbis.se/dataset/{}/download to download files. """.format(dataset.full_name, dataset.short_name) msg.attach(MIMEText(body, 'plain')) - server = smtplib.SMTP(settings.mail_server) + server = smtplib.SMTP(settings.mail_server) # pylint: disable=no-member server.sendmail(msg['from'], [msg['to']], msg.as_string()) - except smtplib.SMTPException as e: - logging.error("Email error: {}".format(e)) - except socket.gaierror as e: - logging.error("Email error: {}".format(e)) + except smtplib.SMTPException as err: + logging.error(f"Email error: {err}") + except socket.gaierror as err: + logging.error(f"Email error: {err}") self.finish() class RevokeUser(handlers.AdminHandler): - def post(self, dataset, email): + def post(self, dataset, email): # pylint: disable=no-self-use dataset, _ = utils.parse_dataset(dataset) with db.database.atomic(): dataset = db.get_dataset(dataset) user = db.User.select().where(db.User.email == email).get() - db.UserAccessLog.create( - user = user, - dataset = dataset, - action = 'access_revoked' - ) + db.UserAccessLog.create(user=user, + dataset=dataset, + action='access_revoked') + def _build_json_response(query, access_for): json_response = [] for user in query: - applyDate = '-' + apply_date = '-' access = access_for(user) if not access: continue access = access[0] if access.access_requested: - applyDate = access.access_requested.strftime('%Y-%m-%d') + apply_date = access.access_requested.strftime('%Y-%m-%d') - data = { - 'user': user.name, - 'email': user.email, + data = {'user': user.name, + 'email': user.email, 'affiliation': user.affiliation, - 'country': user.country, - 'newsletter': access.wants_newsletter, - 'has_access': access.has_access, - 'applyDate': applyDate - } + 'country': user.country, + 'newsletter': access.wants_newsletter, + 'has_access': access.has_access, + 'applyDate': apply_date} json_response.append(data) return json_response @@ -532,10 +505,8 @@ def get(self, dataset): dataset = db.get_dataset(dataset) users = db.User.select() access = (db.DatasetAccessPending - .select() - .where( - db.DatasetAccessPending.dataset == dataset, - )) + .select() + .where(db.DatasetAccessPending.dataset == dataset)) query = peewee.prefetch(users, access) self.finish({'data': _build_json_response(query, lambda u: u.access_pending)}) @@ -546,41 +517,36 @@ def get(self, dataset): dataset, _ = utils.parse_dataset(dataset) dataset = db.get_dataset(dataset) users = db.User.select() - access = (db.DatasetAccessCurrent - .select() - .where( - db.DatasetAccessCurrent.dataset == dataset, - )) + access = (db.DatasetAccessCurrent.select() + .where(db.DatasetAccessCurrent.dataset == dataset)) query = peewee.prefetch(users, access) - self.finish({'data': _build_json_response( - query, lambda u: u.access_current)}) + self.finish({'data': sorted(_build_json_response( + query, lambda u: u.access_current), key=lambda u: u['applyDate'])}) class UserDatasetAccess(handlers.SafeHandler): def get(self): user = self.current_user - ret = { - "data": [], - } + ret = {"data": []} for access in user.access_pending: - d = {} - d['short_name'] = access.dataset.short_name - d['wants_newsletter'] = access.wants_newsletter - d['is_admin'] = False - d['access'] = False + accessp_dict = {} + accessp_dict['short_name'] = access.dataset.short_name + accessp_dict['wants_newsletter'] = access.wants_newsletter + accessp_dict['is_admin'] = False + accessp_dict['access'] = False - ret['data'].append( d ) + ret['data'].append(accessp_dict) for access in user.access_current: - d = {} - d['short_name'] = access.dataset.short_name - d['wants_newsletter'] = access.wants_newsletter - d['is_admin'] = access.is_admin - d['access'] = True + accessc_dict = {} + accessc_dict['short_name'] = access.dataset.short_name + accessc_dict['wants_newsletter'] = access.wants_newsletter + accessc_dict['is_admin'] = access.is_admin + accessc_dict['access'] = True - ret['data'].append( d ) + ret['data'].append(accessc_dict) self.finish(ret) @@ -589,13 +555,10 @@ class ServeLogo(handlers.UnsafeHandler): def get(self, dataset): dataset, _ = utils.parse_dataset(dataset) try: - logo_entry = db.DatasetLogo.select( - db.DatasetLogo - ).join( - db.Dataset - ).where( - db.Dataset.short_name == dataset - ).get() + logo_entry = (db.DatasetLogo.select(db.DatasetLogo) + .join(db.Dataset) + .where(db.Dataset.short_name == dataset) + .get()) except db.DatasetLogo.DoesNotExist: self.send_error(status_code=404) return @@ -606,15 +569,11 @@ def get(self, dataset): class SFTPAccess(handlers.SafeHandler): - """ - Creates, or re-enables, sFTP users in the database. - """ + """Creates, or re-enables, sFTP users in the database.""" def get(self): - """ - Returns sFTP credentials for the current user. - """ + """Returns sFTP credentials for the current user.""" if db.get_admin_datasets(self.current_user).count() <= 0: - self.finish({'user':None, 'expires':None, 'password':None}) + self.finish({'user': None, 'expires': None, 'password': None}) return password = None @@ -629,9 +588,9 @@ def get(self): # Otherwise return empty values pass - self.finish({'user':username, - 'expires':expires, - 'password':password}) + self.finish({'user': username, + 'expires': expires, + 'password': password}) def post(self): """ @@ -640,7 +599,7 @@ def post(self): new password and expiry date. """ if db.get_admin_datasets(self.current_user).count() <= 0: - self.finish({'user':None, 'expires':None, 'password':None}) + self.finish({'user': None, 'expires': None, 'password': None}) return # Create a new password @@ -654,26 +613,33 @@ def post(self): try: self.current_user.sftp_user.get() # if we have a user, update it - db.SFTPUser.update(password_hash = passwd_hash, - account_expires = expires - ).where(db.SFTPUser.user == self.current_user).execute() + (db.SFTPUser.update(password_hash=passwd_hash, + account_expires=expires) + .where(db.SFTPUser.user == self.current_user) + .execute()) except db.SFTPUser.DoesNotExist: # if there is no user, insert the user in the database - db.SFTPUser.insert(user = self.current_user, - user_uid = db.get_next_free_uid(), - user_name = username, - password_hash = passwd_hash, - account_expires = expires - ).execute() - - self.finish({'user':username, - 'expires':expires.strftime("%Y-%m-%d %H:%M"), - 'password':password}) - - def generate_password(self, size = 12): + (db.SFTPUser.insert(user=self.current_user, # pylint: disable=no-value-for-parameter + user_uid=db.get_next_free_uid(), + user_name=username, + password_hash=passwd_hash, + account_expires=expires).execute()) + + self.finish({'user': username, + 'expires': expires.strftime("%Y-%m-%d %H:%M"), + 'password': password}) + + def generate_password(self, size: int = 12) -> str: # pylint: disable=no-self-use """ Generates a password of length 'size', comprised of random lowercase and uppercase letters, and numbers. + + Args: + size: The length of the password that will be generated + + Returns: + str: The generated password + """ chars = string.ascii_letters + string.digits return ''.join(random.SystemRandom().choice(chars) for _ in range(size)) diff --git a/backend/auth.py b/backend/auth.py index 7f1586b1e..eaefa63fa 100644 --- a/backend/auth.py +++ b/backend/auth.py @@ -1,12 +1,14 @@ -import logging -import handlers -from handlers import BaseHandler -import tornado.auth -import urllib.parse +"""Authentication handlers.""" + import base64 +import logging import uuid -import db -import peewee +import urllib.parse + +import tornado.auth + +from handlers import BaseHandler + class DeveloperLoginHandler(BaseHandler): def get(self): @@ -15,9 +17,9 @@ def get(self): elif not self.get_argument("email", False): self.send_error(status_code=403) - self.set_secure_cookie('user', self.get_argument("user")) - self.set_secure_cookie('email', self.get_argument("email")) - self.set_secure_cookie('identity', self.get_argument("email")) + self.set_secure_cookie('user', self.get_argument("user")) # pylint: disable=no-value-for-parameter + self.set_secure_cookie('email', self.get_argument("email")) # pylint: disable=no-value-for-parameter + self.set_secure_cookie('identity', self.get_argument("email")) # pylint: disable=no-value-for-parameter self.finish() @@ -30,10 +32,10 @@ def get(self): class ElixirLoginHandler(BaseHandler, tornado.auth.OAuth2Mixin): - _OAUTH_AUTHORIZE_URL = "https://login.elixir-czech.org/oidc/authorize" - _OAUTH_ACCESS_TOKEN_URL = "https://login.elixir-czech.org/oidc/token" + _OAUTH_AUTHORIZE_URL = "https://login.elixir-czech.org/oidc/authorize" + _OAUTH_ACCESS_TOKEN_URL = "https://login.elixir-czech.org/oidc/token" _OAUTH_USERINFO_ENDPOINT = "https://login.elixir-czech.org/oidc/userinfo" - _OAUTH_SETTINGS_KEY = 'elixir_oauth' + _OAUTH_SETTINGS_KEY = 'elixir_oauth' def _generate_state(self): state = uuid.uuid4().hex @@ -52,13 +54,19 @@ async def get(self): self.redirect("/security_warning") return - user_token = await self.get_user_token(self.get_argument('code')) - user = await self.get_user(user_token["access_token"]) - - self.set_secure_cookie('access_token', user_token["access_token"]) - self.set_secure_cookie('user', user["name"]) - self.set_secure_cookie('email', user["email"]) - self.set_secure_cookie('identity', user["sub"]) + user_token = await self.get_user_token(self.get_argument('code')) # pylint: disable=no-value-for-parameter + user = await self.get_user(user_token["access_token"]) + + try: + self.set_secure_cookie('access_token', user_token["access_token"]) + self.set_secure_cookie('user', user["name"]) + self.set_secure_cookie('email', user["email"]) + self.set_secure_cookie('identity', user["sub"]) + except KeyError as err: + logging.error(f'ElixirLoginHandler: data missing ({err}); user: {user}' + + f', user_token: {user_token}') + self.redirect("/error") + return redirect = self.get_secure_cookie("login_redirect") self.clear_cookie("login_redirect") @@ -67,73 +75,58 @@ async def get(self): self.redirect(redirect) elif self.get_argument("error", False): - logging.error("Elixir error: {}".format( self.get_argument("error") )) - logging.error(" Description: {}".format( self.get_argument("error_description") )) + logging.error("Elixir error: {}".format(self.get_argument("error"))) # pylint: disable=no-value-for-parameter + logging.error(" Description: {}".format(self.get_argument("error_description"))) # pylint: disable=no-value-for-parameter - self.set_user_msg("Elixir Error: %s, %s" % (self.get_argument("error"), - self.get_argument("error_description"))) + self.set_user_msg(f"Elixir Error: ,{self.get_argument('error')} " + # pylint: disable=no-value-for-parameter + f"{self.get_argument('error_description')}") # pylint: disable=no-value-for-parameter self.redirect("/error") else: self.set_secure_cookie('login_redirect', self.get_argument("next", '/'), 1) state = self._generate_state() - self.authorize_redirect( - redirect_uri = self.settings['elixir_oauth']['redirect_uri'], - client_id = self.settings['elixir_oauth']['id'], - scope = ['openid', 'profile', 'email', 'bona_fide_status'], - response_type = 'code', - extra_params = {'state': state} - ) + self.authorize_redirect(redirect_uri=self.settings['elixir_oauth']['redirect_uri'], + client_id=self.settings['elixir_oauth']['id'], + scope=['openid', 'profile', 'email', 'bona_fide_status'], + response_type='code', + extra_params={'state': state}) async def get_user(self, access_token): http = self.get_auth_http_client() - response = await http.fetch( - self._OAUTH_USERINFO_ENDPOINT, - headers = { - 'Content-Type': 'application/x-www-form-urlencoded', - 'Authorization': "Bearer {}".format(access_token), - } - ) + response = await http.fetch(self._OAUTH_USERINFO_ENDPOINT, + headers={'Content-Type': 'application/x-www-form-urlencoded', + 'Authorization': "Bearer {}".format(access_token)}) if response.error: - logging.error("get_user error: {}".format(response)) + logging.error(f"get_user error: {response}") return - return tornado.escape.json_decode( response.body ) + return tornado.escape.json_decode(response.body) async def get_user_token(self, code): redirect_uri = self.settings['elixir_oauth']['redirect_uri'] http = self.get_auth_http_client() - body = urllib.parse.urlencode({ - "redirect_uri": redirect_uri, - "code": code, - "grant_type": "authorization_code", - }) + body = urllib.parse.urlencode({"redirect_uri": redirect_uri, + "code": code, + "grant_type": "authorization_code"}) client_id = self.settings['elixir_oauth']['id'] - secret = self.settings['elixir_oauth']['secret'] - - authorization = base64.b64encode( - bytes("{}:{}".format(client_id, secret), - 'ascii' ) - ).decode('ascii') - - response = await http.fetch( - self._OAUTH_ACCESS_TOKEN_URL, - method = "POST", - body = body, - headers = { - 'Content-Type': 'application/x-www-form-urlencoded', - 'Authorization': "Basic {}".format(authorization), - }, - ) + secret = self.settings['elixir_oauth']['secret'] + + authorization = base64.b64encode(bytes(f"{client_id}: {secret}", 'ascii')).decode('ascii') + + response = await http.fetch(self._OAUTH_ACCESS_TOKEN_URL, + method="POST", + body=body, + headers={'Content-Type': 'application/x-www-form-urlencoded', + 'Authorization': "Basic {}".format(authorization)}) if response.error: - logging.error("get_user_token error: {}".format(response)) + logging.error(f"get_user_token error: {response}") return - return tornado.escape.json_decode( response.body ) + return tornado.escape.json_decode(response.body) class ElixirLogoutHandler(BaseHandler): @@ -142,5 +135,3 @@ def get(self): redirect = self.get_argument("next", '/') self.redirect(redirect) - - diff --git a/backend/db.py b/backend/db.py index 08cc6a998..679bdc2cf 100644 --- a/backend/db.py +++ b/backend/db.py @@ -1,9 +1,8 @@ #!/usr/bin/env python3 import logging -import settings -from peewee import (BigIntegerField, - BlobField, + +from peewee import (BlobField, BooleanField, CharField, DateTimeField, @@ -12,20 +11,20 @@ FloatField, ForeignKeyField, Model, - PostgresqlDatabase, - PrimaryKeyField, - SQL, TextField, - fn, - ) + fn) from playhouse.postgres_ext import ArrayField, BinaryJSONField, PostgresqlExtDatabase +import settings + +# pylint: disable=no-member database = PostgresqlExtDatabase(settings.psql_name, - user = settings.psql_user, - password = settings.psql_pass, - host = settings.psql_host, - port = settings.psql_port, - register_hstore = False) + user=settings.psql_user, + password=settings.psql_pass, + host=settings.psql_host, + port=settings.psql_port, + register_hstore=False) +# pylint: enable=no-member class BaseModel(Model): class Meta: @@ -33,7 +32,7 @@ class Meta: class EnumField(Field): - db_field = 'string' # The same as for CharField + db_field = 'string' # The same as for CharField def __init__(self, choices=None, *args, **kwargs): self.values = choices or [] @@ -41,12 +40,12 @@ def __init__(self, choices=None, *args, **kwargs): def db_value(self, value): if value not in self.values: - raise ValueError("Illegal value for '{}'".format(self.db_column)) + raise ValueError("Illegal value for '{}'".format(self.column_name)) return value def python_value(self, value): if value not in self.values: - raise ValueError("Illegal value for '{}'".format(self.db_column)) + raise ValueError("Illegal value for '{}'".format(self.column_name)) return value ### @@ -84,7 +83,8 @@ class Meta: chrom = CharField(max_length=10) start = IntegerField(column_name="start_pos") stop = IntegerField(column_name="end_pos") - strand = EnumField(choices=['+','-']) + strand = EnumField(choices=['+', '-']) + class GeneOtherNames(BaseModel): class Meta: @@ -94,6 +94,7 @@ class Meta: gene = ForeignKeyField(Gene, column_name="gene", backref="other_names") name = CharField(null=True) + class Transcript(BaseModel): class Meta: table_name = 'transcripts' @@ -106,7 +107,7 @@ class Meta: chrom = CharField(max_length=10) start = IntegerField(column_name="start_pos") stop = IntegerField(column_name="stop_pos") - strand = EnumField(choices = ['+', '-']) + strand = EnumField(choices=['+', '-']) class Feature(BaseModel): @@ -119,9 +120,10 @@ class Meta: chrom = CharField(max_length=10) start = IntegerField(column_name="start_pos") stop = IntegerField(column_name="stop_pos") - strand = EnumField(choices = ['+', '-']) + strand = EnumField(choices=['+', '-']) feature_type = CharField() + ### # Study and Dataset fields ## @@ -134,8 +136,8 @@ class Meta: table_name = 'collections' schema = 'data' - name = CharField(column_name="study_name", null = True) - ethnicity = CharField(null = True) + name = CharField(column_name="study_name", null=True) + ethnicity = CharField(null=True) class Study(BaseModel): @@ -147,14 +149,14 @@ class Meta: table_name = 'studies' schema = 'data' - pi_name = CharField() - pi_email = CharField() - contact_name = CharField() - contact_email = CharField() - title = CharField() - description = TextField(column_name="study_description", null=True) + pi_name = CharField() + pi_email = CharField() + contact_name = CharField() + contact_email = CharField() + title = CharField() + description = TextField(column_name="study_description", null=True) publication_date = DateTimeField() - ref_doi = CharField(null=True) + ref_doi = CharField(null=True) class Dataset(BaseModel): @@ -167,17 +169,17 @@ class Meta: table_name = 'datasets' schema = 'data' - study = ForeignKeyField(Study, column_name="study", backref='datasets') - short_name = CharField() - full_name = CharField() - browser_uri = CharField(null=True) - beacon_uri = CharField(null=True) - description = TextField(column_name="beacon_description", null=True) - avg_seq_depth = FloatField(null=True) - seq_type = CharField(null=True) - seq_tech = CharField(null=True) - seq_center = CharField(null=True) - dataset_size = IntegerField() + study = ForeignKeyField(Study, column_name="study", backref='datasets') + short_name = CharField() + full_name = CharField() + browser_uri = CharField(null=True) + beacon_uri = CharField(null=True) + description = TextField(column_name="beacon_description", null=True) + avg_seq_depth = FloatField(null=True) + seq_type = CharField(null=True) + seq_tech = CharField(null=True) + seq_center = CharField(null=True) + dataset_size = IntegerField() def has_image(self): try: @@ -192,10 +194,10 @@ class Meta: table_name = 'sample_sets' schema = 'data' - dataset = ForeignKeyField(Dataset, column_name="dataset", backref='sample_sets') - collection = ForeignKeyField(Collection, column_name="collection", backref='sample_sets') + dataset = ForeignKeyField(Dataset, column_name="dataset", backref='sample_sets') + collection = ForeignKeyField(Collection, column_name="collection", backref='sample_sets') sample_size = IntegerField() - phenotype = CharField(null=True) + phenotype = CharField(null=True) class DatasetVersion(BaseModel): @@ -203,20 +205,24 @@ class Meta: table_name = 'dataset_versions' schema = 'data' - dataset = ForeignKeyField(Dataset, column_name="dataset", backref='versions') - reference_set = ForeignKeyField(ReferenceSet, column_name="reference_set", backref='dataset_versions') - version = CharField(column_name="dataset_version") - description = TextField(column_name="dataset_description") - terms = TextField() - available_from = DateTimeField() - ref_doi = CharField(null=True) + dataset = ForeignKeyField(Dataset, column_name="dataset", backref='versions') + reference_set = ForeignKeyField(ReferenceSet, + column_name="reference_set", + backref='dataset_versions') + version = CharField(column_name="dataset_version") + description = TextField(column_name="dataset_description") + terms = TextField() + available_from = DateTimeField() + ref_doi = CharField(null=True) data_contact_name = CharField(null=True) data_contact_link = CharField(null=True) - num_variants = IntegerField(null=True) - coverage_levels = ArrayField(IntegerField, null=True) + num_variants = IntegerField(null=True) + coverage_levels = ArrayField(IntegerField, null=True) portal_avail = BooleanField(null=True) - file_access = EnumField(null=False, choices=['PRIVATE', 'CONTROLLED', 'REGISTERED', 'PUBLIC']) - beacon_access = EnumField(null=False, choices=['PRIVATE', 'CONTROLLED', 'REGISTERED', 'PUBLIC']) + file_access = EnumField(null=False, choices=['PRIVATE', 'CONTROLLED', + 'REGISTERED', 'PUBLIC']) + beacon_access = EnumField(null=False, choices=['PRIVATE', 'CONTROLLED', + 'REGISTERED', 'PUBLIC']) class DatasetFile(BaseModel): @@ -224,10 +230,12 @@ class Meta: table_name = 'dataset_files' schema = 'data' - dataset_version = ForeignKeyField(DatasetVersion, column_name="dataset_version", backref='files') - name = CharField(column_name="basename") - uri = CharField() - file_size = IntegerField() + dataset_version = ForeignKeyField(DatasetVersion, + column_name="dataset_version", + backref='files') + name = CharField(column_name="basename") + uri = CharField() + file_size = IntegerField() class DatasetLogo(BaseModel): @@ -235,9 +243,9 @@ class Meta: table_name = 'dataset_logos' schema = 'data' - dataset = ForeignKeyField(Dataset, column_name="dataset", backref='logo') - mimetype = CharField() - data = BlobField(column_name="bytes") + dataset = ForeignKeyField(Dataset, column_name="dataset", backref='logo') + mimetype = CharField() + data = BlobField(column_name="bytes") ### @@ -249,7 +257,9 @@ class Meta: table_name = "variants" schema = 'data' - dataset_version = ForeignKeyField(DatasetVersion, column_name="dataset_version", backref="variants") + dataset_version = ForeignKeyField(DatasetVersion, + column_name="dataset_version", + backref="variants") rsid = IntegerField() chrom = CharField(max_length=10) pos = IntegerField() @@ -269,10 +279,12 @@ class Meta: class VariantMate(BaseModel): class Meta: - table_name = "mate" + table_name = "mates" schema = 'data' - dataset_version = ForeignKeyField(DatasetVersion, column_name="dataset_version", backref="mate") + dataset_version = ForeignKeyField(DatasetVersion, + column_name="dataset_version", + backref="mates") chrom = CharField(max_length=10) pos = IntegerField() ref = CharField() @@ -344,23 +356,23 @@ class Meta: table_name = "users" schema = 'users' - name = CharField(column_name="username", null=True) - email = CharField(unique=True) - identity = CharField(unique=True) + name = CharField(column_name="username", null=True) + email = CharField(unique=True) + identity = CharField(unique=True) identity_type = EnumField(null=False, choices=['google', 'elixir'], default='elixir') - affiliation = CharField(null=True) - country = CharField(null=True) + affiliation = CharField(null=True) + country = CharField(null=True) def is_admin(self, dataset): - return DatasetAccess.select().where( - DatasetAccess.dataset == dataset, - DatasetAccess.user == self, - DatasetAccess.is_admin - ).count() + return (DatasetAccess.select() + .where(DatasetAccess.dataset == dataset, + DatasetAccess.user == self, + DatasetAccess.is_admin) + .count()) def has_access(self, dataset, ds_version=None): """ - Check whether user has permission to access a dataset + Check whether user has permission to access a dataset. Args: dataset (Database): peewee Database object @@ -375,7 +387,7 @@ def has_access(self, dataset, ds_version=None): return False if dsv.file_access in ('REGISTERED', 'PUBLIC'): return True - elif dsv.file_access == 'PRIVATE': + if dsv.file_access == 'PRIVATE': return False return (DatasetAccessCurrent.select() @@ -384,10 +396,10 @@ def has_access(self, dataset, ds_version=None): .count()) > 0 def has_requested_access(self, dataset): - return DatasetAccessPending.select().where( - DatasetAccessPending.dataset == dataset, - DatasetAccessPending.user == self - ).count() + return (DatasetAccessPending.select() + .where(DatasetAccessPending.dataset == dataset, + DatasetAccessPending.user == self) + .count()) class SFTPUser(BaseModel): @@ -395,9 +407,9 @@ class Meta: table_name = "sftp_users" schema = 'users' - user = ForeignKeyField(User, backref='sftp_user') - user_uid = IntegerField(unique=True) - user_name = CharField(null=False) + user = ForeignKeyField(User, backref='sftp_user') + user_uid = IntegerField(unique=True) + user_name = CharField(null=False) password_hash = CharField(null=False) account_expires = DateTimeField(null=False) @@ -407,10 +419,11 @@ class Meta: table_name = "user_access_log" schema = 'users' - user = ForeignKeyField(User, backref='access_logs') - dataset = ForeignKeyField(Dataset, column_name='dataset', backref='access_logs') - action = EnumField(null=True, choices=['access_granted','access_revoked','access_requested','private_link']) - ts = DateTimeField() + user = ForeignKeyField(User, backref='access_logs') + dataset = ForeignKeyField(Dataset, column_name='dataset', backref='access_logs') + action = EnumField(null=True, choices=['access_granted', 'access_revoked', + 'access_requested', 'private_link']) + ts = DateTimeField() class UserConsentLog(BaseModel): @@ -418,9 +431,11 @@ class Meta: table_name = "user_consent_log" schema = 'users' - user = ForeignKeyField(User, backref='consent_logs') - dataset_version = ForeignKeyField(DatasetVersion, column_name='dataset_version', backref='consent_logs') - ts = DateTimeField() + user = ForeignKeyField(User, backref='consent_logs') + dataset_version = ForeignKeyField(DatasetVersion, + column_name='dataset_version', + backref='consent_logs') + ts = DateTimeField() class UserDownloadLog(BaseModel): @@ -428,9 +443,11 @@ class Meta: table_name = "user_download_log" schema = 'users' - user = ForeignKeyField(User, backref='download_logs') - dataset_file = ForeignKeyField(DatasetFile, column_name='dataset_file', backref='download_logs') - ts = DateTimeField() + user = ForeignKeyField(User, backref='download_logs') + dataset_file = ForeignKeyField(DatasetFile, + column_name='dataset_file', + backref='download_logs') + ts = DateTimeField() class DatasetAccess(BaseModel): @@ -438,10 +455,10 @@ class Meta: table_name = "dataset_access" schema = 'users' - dataset = ForeignKeyField(Dataset, column_name='dataset', backref='access') - user = ForeignKeyField(User, backref='dataset_access') + dataset = ForeignKeyField(Dataset, column_name='dataset', backref='access') + user = ForeignKeyField(User, backref='dataset_access') wants_newsletter = BooleanField(null=True) - is_admin = BooleanField(null=True) + is_admin = BooleanField(null=True) class Linkhash(BaseModel): @@ -449,10 +466,12 @@ class Meta: table_name = "linkhash" schema = 'users' - dataset_version = ForeignKeyField(DatasetVersion, column_name='dataset_version', backref='link_hashes') - user = ForeignKeyField(User, backref='link_hashes') - hash = CharField() - expires_on = DateTimeField() + dataset_version = ForeignKeyField(DatasetVersion, + column_name='dataset_version', + backref='link_hashes') + user = ForeignKeyField(User, backref='link_hashes') + hash = CharField() + expires_on = DateTimeField() class BeaconCounts(BaseModel): @@ -460,8 +479,8 @@ class Meta: table_name = "beacon_dataset_counts_table" schema = 'beacon' - datasetid = CharField(primary_key=True) - callcount = IntegerField() + datasetid = CharField(primary_key=True) + callcount = IntegerField() variantcount = IntegerField() @@ -474,8 +493,10 @@ class Meta: table_name = 'dataset_version_current' schema = 'data' - dataset = ForeignKeyField(Dataset, column_name="dataset", backref='current_version') - reference_set = ForeignKeyField(ReferenceSet, column_name="reference_set", backref='current_version') + dataset = ForeignKeyField(Dataset, column_name="dataset", backref='current_version') + reference_set = ForeignKeyField(ReferenceSet, + column_name="reference_set", + backref='current_version') class DatasetAccessCurrent(DatasetAccess): @@ -483,9 +504,9 @@ class Meta: table_name = 'dataset_access_current' schema = 'users' - dataset = ForeignKeyField(Dataset, column_name='dataset', backref='access_current') - user = ForeignKeyField(User, backref='access_current') - has_access = IntegerField() + dataset = ForeignKeyField(Dataset, column_name='dataset', backref='access_current') + user = ForeignKeyField(User, backref='access_current') + has_access = IntegerField() access_requested = DateTimeField() @@ -494,22 +515,24 @@ class Meta: table_name = 'dataset_access_pending' schema = 'users' - dataset = ForeignKeyField(Dataset, column_name='dataset', backref='access_pending') - user = ForeignKeyField(User, backref='access_pending') - has_access = IntegerField() + dataset = ForeignKeyField(Dataset, column_name='dataset', backref='access_pending') + user = ForeignKeyField(User, backref='access_pending') + has_access = IntegerField() access_requested = DateTimeField() + ##### # Help functions ## -def get_next_free_uid(): +def get_next_free_uid() -> int: """ - Get the next free uid >= 10000 and > than the current uids + Get the next free uid >= 10000 and > than the current uids from the sftp_user table in the db. Returns: int: the next free uid + """ default = 10000 next_uid = default @@ -532,11 +555,12 @@ def get_admin_datasets(user): Returns: DataSetAccess: + """ - return DatasetAccess.select().where( DatasetAccess.user == user, DatasetAccess.is_admin) + return DatasetAccess.select().where(DatasetAccess.user == user, DatasetAccess.is_admin) -def get_dataset(dataset:str): +def get_dataset(dataset: str): """ Given dataset name get Dataset @@ -545,12 +569,13 @@ def get_dataset(dataset:str): Returns: Dataset: the corresponding DatasetVersion entry + """ - dataset = Dataset.select().where( Dataset.short_name == dataset).get() + dataset = Dataset.select().where(Dataset.short_name == dataset).get() return dataset -def get_dataset_version(dataset:str, version:str=None): +def get_dataset_version(dataset: str, version: str = None): """ Given dataset get DatasetVersion @@ -559,6 +584,7 @@ def get_dataset_version(dataset:str, version:str=None): Returns: DatasetVersion: the corresponding DatasetVersion entry + """ if version: try: @@ -568,9 +594,9 @@ def get_dataset_version(dataset:str, version:str=None): .where(DatasetVersion.version == version, Dataset.short_name == dataset)).get() except DatasetVersion.DoesNotExist: - logging.error("get_dataset_version({}, {}): ".format(dataset, version) + - "cannot retrieve dataset version") - return + logging.error(f"get_dataset_version(%s, %s): " + + "cannot retrieve dataset version", dataset, version) + return None else: try: dataset_version = (DatasetVersionCurrent @@ -578,17 +604,18 @@ def get_dataset_version(dataset:str, version:str=None): .join(Dataset) .where(Dataset.short_name == dataset)).get() except DatasetVersionCurrent.DoesNotExist: - logging.error("get_dataset_version({}, version=None): ".format(dataset) + + logging.error(f"get_dataset_version({dataset}, version=None): " + "cannot retrieve dataset version") - return + return None return dataset_version -def build_dict_from_row(row): - d = {} +def build_dict_from_row(row) -> dict: + """Build a dictionary from a row object""" + outdict = {} for field, value in row.__dict__['__data__'].items(): if field == "id": continue - d[field] = value - return d + outdict[field] = value + return outdict diff --git a/backend/handlers.py b/backend/handlers.py index 5c171eb0f..fcb5710b0 100644 --- a/backend/handlers.py +++ b/backend/handlers.py @@ -1,13 +1,14 @@ import logging -import peewee -import tornado.auth -import tornado.web -import tornado.escape -import tornado.httpclient import os.path import datetime import urllib.parse + +import peewee +import tornado.auth +import tornado.escape from tornado.escape import json_encode +import tornado.httpclient +import tornado.web import db @@ -19,13 +20,13 @@ class directly but from either SafeHandler or UnsafeHandler to make security status explicit. """ def prepare(self): - ## Make sure we have the xsrf_token, this will generate the xsrf cookie if it isn't set - self.xsrf_token #pylint: disable=pointless-statement + # Make sure we have the xsrf_token, this will generate the xsrf cookie if it isn't set + self.xsrf_token # pylint: disable=pointless-statement if db.database.is_closed(): try: db.database.connect() - except peewee.DatabaseError as e: - logging.error("Failed to connect to database: {}".format(e)) + except peewee.DatabaseError as err: + logging.error(f"Failed to connect to database: {err}") def on_finish(self): if not db.database.is_closed(): @@ -33,7 +34,7 @@ def on_finish(self): def get_current_user(self): email = self.get_secure_cookie('email') - name = self.get_secure_cookie('user') + name = self.get_secure_cookie('user') identity = self.get_secure_cookie('identity') # Fix ridiculous bug with quotation marks showing on the web @@ -42,15 +43,15 @@ def get_current_user(self): if identity: try: - return db.User.select().where( db.User.identity == identity ).get() + return db.User.select().where(db.User.identity == identity).get() except db.User.DoesNotExist: - ## Not saved in the database yet + # Not saved in the database yet try: - return db.User(email = email.decode('utf-8'), - name = name.decode('utf-8'), - identity = identity.decode('utf-8')) - except peewee.OperationalError as e: - logging.error("Can't create new user: {}".format(e)) + return db.User(email=email.decode('utf-8'), + name=name.decode('utf-8'), + identity=identity.decode('utf-8')) + except peewee.OperationalError as err: + logging.error(f"Can't create new user: {err}") else: return None @@ -62,7 +63,7 @@ def set_user_msg(self, msg, level="info"): """ if level not in ["success", "info", "warning", "error"]: level = "info" - self.set_cookie("msg", urllib.parse.quote( json_encode({"msg":msg, "level":level}) ) ) + self.set_cookie("msg", urllib.parse.quote(json_encode({"msg": msg, "level": level}))) def write_error(self, status_code, **kwargs): """ @@ -78,6 +79,7 @@ def write(self, chunk): new_chunk = _convert_keys_to_hump_back(chunk) super().write(new_chunk) + def _convert_keys_to_hump_back(chunk): """ Converts keys given in snake_case to humpBack-case, while preserving the @@ -128,7 +130,7 @@ def prepare(self): return kwargs = self.path_kwargs - if not 'dataset' in kwargs: + if 'dataset' not in kwargs: logging.debug("No dataset: Send error 403") self.send_error(status_code=403) return @@ -152,7 +154,7 @@ def prepare(self): logging.debug("No dataset: Send error 403") self.send_error(status_code=403) return - if not self.current_user.is_admin( db.get_dataset(kwargs['dataset']) ): + if not self.current_user.is_admin(db.get_dataset(kwargs['dataset'])): logging.debug("No user admin: Send error 403") self.send_error(status_code=403) return @@ -198,7 +200,7 @@ def get(self, dataset, file, ds_version=None, user=None): self.send_error(status_code=403) return - db.UserDownloadLog.create(user = user, dataset_file = dbfile) + db.UserDownloadLog.create(user=user, dataset_file=dbfile) abspath = os.path.abspath(os.path.join(self.root, file)) self.set_header("X-Accel-Redirect", abspath) @@ -226,21 +228,19 @@ class AuthorizedStaticNginxFileHandler(AuthorizedHandler, BaseStaticNginxFileHan class TemporaryStaticNginxFileHandler(BaseStaticNginxFileHandler): def get(self, dataset, ds_version, hash_value, file): logging.debug("Want to download hash {} ({})".format(hash_value, file)) - linkhash = (db.Linkhash - .select() - .join(db.DatasetVersion) - .join(db.DatasetFile) - .where(db.Linkhash.hash == hash_value, - db.Linkhash.expires_on > datetime.datetime.now(), - db.DatasetFile.name == file)) + linkhash = (db.Linkhash.select() + .join(db.DatasetVersion) + .join(db.DatasetFile) + .where(db.Linkhash.hash == hash_value, + db.Linkhash.expires_on > datetime.datetime.now(), + db.DatasetFile.name == file)) if linkhash.count() > 0: logging.debug("Linkhash valid") # Get temporary user from hash_value - user = (db.User - .select(db.User) - .join(db.Linkhash) - .where(db.Linkhash.hash == hash_value) - ).get() + user = (db.User.select(db.User) + .join(db.Linkhash) + .where(db.Linkhash.hash == hash_value) + .get()) super().get(dataset, file, ds_version, user) else: logging.debug("Linkhash invalid") diff --git a/backend/modules/browser/browser_handlers.py b/backend/modules/browser/browser_handlers.py index 26da598b4..3a726d068 100644 --- a/backend/modules/browser/browser_handlers.py +++ b/backend/modules/browser/browser_handlers.py @@ -13,7 +13,7 @@ class Autocomplete(handlers.UnsafeHandler): """Provide autocompletion for protein names based on current query.""" - def get(self, dataset:str, query:str, ds_version:str=None): + def get(self, dataset: str, query: str, ds_version: str = None): """ Provide autocompletion for protein names based on current query. @@ -21,6 +21,7 @@ def get(self, dataset:str, query:str, ds_version:str=None): dataset (str): dataset short name query (str): query ds_version (str): dataset version + """ dataset, ds_version = utils.parse_dataset(dataset, ds_version) ret = {} @@ -34,7 +35,8 @@ def get(self, dataset:str, query:str, ds_version:str=None): class Download(handlers.UnsafeHandler): """Download variants in CSV format.""" - def get(self, dataset:str, datatype:str, item:str, ds_version:str=None, filter_type:str=None): + def get(self, dataset: str, datatype: str, item: str, # pylint: disable=too-many-arguments + ds_version: str = None, filter_type: str = None): """ Download variants in CSV format. @@ -46,25 +48,29 @@ def get(self, dataset:str, datatype:str, item:str, ds_version:str=None, filter_t item (str): query item ds_version (str): dataset version filter_type (str): type of filter to apply + """ # ctrl.filterVariantsBy~ctrl.filterIncludeNonPass dataset, ds_version = utils.parse_dataset(dataset, ds_version) - filename = "{}_{}_{}.csv".format(dataset, datatype, item) - self.set_header('Content-Type','text/csv') - self.set_header('content-Disposition','attachement; filename={}'.format(filename)) + filename = f'{dataset}_{datatype}_{item}.csv' + self.set_header('Content-Type', 'text/csv') + self.set_header(f'content-Disposition', + f'attachment; filename={filename}') data = utils.get_variant_list(dataset, datatype, item, ds_version) # filter variants based on what is shown if filter_type: filters = filter_type.split('~') if filters[1] == 'false': - data['variants'] = [variant for variant in data['variants'] if variant['filter_string'] == 'PASS'] + data['variants'] = [variant for variant in data['variants'] + if variant['filter_string'] == 'PASS'] if filters[0] == 'mislof': data['variants'] = [variant for variant in data['variants'] if variant['major_consequence'] == 'missense' or 'LoF' in variant['flags']] elif 'lof' in filters[0]: - data['variants'] = [variant for variant in data['variants'] if 'LoF' in variant['flags']] + data['variants'] = [variant for variant in data['variants'] + if 'LoF' in variant['flags']] # Write header self.write(','.join([h[1] for h in data['headers']]) + '\n') @@ -77,7 +83,7 @@ def get(self, dataset:str, datatype:str, item:str, ds_version:str=None, filter_t class GetCoverage(handlers.UnsafeHandler): """Retrieve coverage.""" - def get(self, dataset:str, datatype:str, item:str, ds_version:str=None): + def get(self, dataset: str, datatype: str, item: str, ds_version: str = None): """ Retrieve coverage. @@ -86,6 +92,7 @@ def get(self, dataset:str, datatype:str, item:str, ds_version:str=None): datatype (str): type of data item (str): query item ds_version (str): dataset version + """ dataset, ds_version = utils.parse_dataset(dataset, ds_version) try: @@ -102,7 +109,7 @@ def get(self, dataset:str, datatype:str, item:str, ds_version:str=None): class GetCoveragePos(handlers.UnsafeHandler): """Retrieve coverage range.""" - def get(self, dataset:str, datatype:str, item:str, ds_version:str=None): + def get(self, dataset: str, datatype: str, item: str, ds_version: str = None): """ Retrieve coverage range. @@ -111,13 +118,16 @@ def get(self, dataset:str, datatype:str, item:str, ds_version:str=None): datatype (str): type of data item (str): query item ds_version (str): dataset version + """ dataset, ds_version = utils.parse_dataset(dataset, ds_version) try: ret = utils.get_coverage_pos(dataset, datatype, item, ds_version) - except ValueError: - logging.error('GetCoveragePos: unable to parse region ({})'.format(item)) - self.send_error(status_code=400, reason='Unable to parse region') + except error.NotFoundError as err: + self.send_error(status_code=404, reason=str(err)) + return + except (error.ParsingError, error.MalformedRequest) as err: + self.send_error(status_code=400, reason=str(err)) return self.finish(ret) @@ -126,7 +136,7 @@ def get(self, dataset:str, datatype:str, item:str, ds_version:str=None): class GetGene(handlers.UnsafeHandler): """Request information about a gene.""" - def get(self, dataset:str, gene:str, ds_version:str=None): + def get(self, dataset: str, gene: str, ds_version: str = None): """ Request information about a gene. @@ -134,11 +144,12 @@ def get(self, dataset:str, gene:str, ds_version:str=None): dataset (str): short name of the dataset gene (str): the gene id ds_version (str): dataset version + """ dataset, ds_version = utils.parse_dataset(dataset, ds_version) gene_id = gene - ret = {'gene':{'gene_id': gene_id}} + ret = {'gene': {'gene_id': gene_id}} # Gene try: @@ -146,27 +157,23 @@ def get(self, dataset:str, gene:str, ds_version:str=None): except error.NotFoundError as err: self.send_error(status_code=404, reason=str(err)) return - except (error.ParsingError, error.MalformedRequest) as err: - self.send_error(status_code=400, reason=str(err)) - return - if not gene: - self.send_error(status_code=404, reason='Gene not found') - return ret['gene'] = gene # Add exons from transcript transcript = lookups.get_transcript(dataset, gene['canonical_transcript'], ds_version) ret['exons'] = [] for exon in sorted(transcript['exons'], key=lambda k: k['start']): - ret['exons'] += [{'start':exon['start'], 'stop':exon['stop'], 'type':exon['feature_type']}] + ret['exons'] += [{'start': exon['start'], + 'stop': exon['stop'], + 'type': exon['feature_type']}] # Transcripts transcripts_in_gene = lookups.get_transcripts_in_gene(dataset, gene_id, ds_version) if transcripts_in_gene: ret['transcripts'] = [] for transcript in transcripts_in_gene: - ret['transcripts'] += [{'transcript_id':transcript['transcript_id']}] + ret['transcripts'] += [{'transcript_id': transcript['transcript_id']}] # temporary fix for names gene['gene_name'] = gene['name'] @@ -178,7 +185,7 @@ def get(self, dataset:str, gene:str, ds_version:str=None): class GetRegion(handlers.UnsafeHandler): """Request information about genes in a region.""" - def get(self, dataset:str, region:str, ds_version:str=None): + def get(self, dataset: str, region: str, ds_version: str = None): """ Request information about genes in a region. @@ -186,6 +193,7 @@ def get(self, dataset:str, region:str, ds_version:str=None): dataset (str): short name of the dataset region (str): the region in the format chr-startpos-endpos ds_version (str): dataset version + """ dataset, ds_version = utils.parse_dataset(dataset, ds_version) @@ -196,11 +204,9 @@ def get(self, dataset:str, region:str, ds_version:str=None): logging.warning('GetRegion: unable to parse region ({})'.format(region)) return - ret = {'region':{'chrom': chrom, - 'start': start, - 'stop': stop, - }, - } + ret = {'region': {'chrom': chrom, + 'start': start, + 'stop': stop}} if utils.is_region_too_large(start, stop): self.send_error(status_code=400, reason='Region too large') @@ -210,17 +216,16 @@ def get(self, dataset:str, region:str, ds_version:str=None): if genes_in_region: ret['region']['genes'] = [] for gene in genes_in_region: - ret['region']['genes'] += [{'gene_id':gene['gene_id'], - 'gene_name':gene['name'], - 'full_gene_name':gene['full_name'], - }] + ret['region']['genes'] += [{'gene_id': gene['gene_id'], + 'gene_name': gene['name'], + 'full_gene_name': gene['full_name']}] self.finish(ret) class GetTranscript(handlers.UnsafeHandler): """Request information about a transcript.""" - def get(self, dataset:str, transcript:str, ds_version:str=None): + def get(self, dataset: str, transcript: str, ds_version: str = None): """ Request information about a transcript. @@ -228,40 +233,39 @@ def get(self, dataset:str, transcript:str, ds_version:str=None): dataset (str): short name of the dataset transcript (str): the transcript id - Returns: - dict: transcript (transcript and exons), gene (gene information) - """ dataset, ds_version = utils.parse_dataset(dataset, ds_version) transcript_id = transcript - ret = {'transcript':{}, - 'gene':{}, - } + ret = {'transcript': {}, + 'gene': {}} # Add transcript information - try: + try: transcript = lookups.get_transcript(dataset, transcript_id, ds_version) except error.NotFoundError as err: self.send_error(status_code=404, reason=str(err)) return - + ret['transcript']['id'] = transcript['transcript_id'] - ret['transcript']['number_of_CDS'] = len([t for t in transcript['exons'] if t['feature_type'] == 'CDS']) + ret['transcript']['number_of_CDS'] = len([t for t in transcript['exons'] + if t['feature_type'] == 'CDS']) # Add exon information ret['exons'] = [] for exon in sorted(transcript['exons'], key=lambda k: k['start']): - ret['exons'] += [{'start':exon['start'], 'stop':exon['stop'], 'type':exon['feature_type']}] + ret['exons'] += [{'start': exon['start'], + 'stop': exon['stop'], + 'type': exon['feature_type']}] # Add gene information - gene = lookups.get_gene_by_dbid(transcript['gene']) - ret['gene']['id'] = gene['gene_id'] - ret['gene']['name'] = gene['name'] - ret['gene']['full_name'] = gene['full_name'] + gene = lookups.get_gene_by_dbid(transcript['gene']) + ret['gene']['id'] = gene['gene_id'] + ret['gene']['name'] = gene['name'] + ret['gene']['full_name'] = gene['full_name'] ret['gene']['canonical_transcript'] = gene['canonical_transcript'] - gene_transcripts = lookups.get_transcripts_in_gene_by_dbid(transcript['gene']) - ret['gene']['transcripts'] = [g['transcript_id'] for g in gene_transcripts] + gene_transcripts = lookups.get_transcripts_in_gene_by_dbid(transcript['gene']) + ret['gene']['transcripts'] = [g['transcript_id'] for g in gene_transcripts] self.finish(ret) @@ -269,31 +273,35 @@ def get(self, dataset:str, transcript:str, ds_version:str=None): class GetVariant(handlers.UnsafeHandler): """Request information about a gene.""" - def get(self, dataset:str, variant:str, ds_version:str=None): + def get(self, dataset: str, variant: str, ds_version: str = None): """ Request information about a gene. Args: dataset (str): short name of the dataset variant (str): variant in the format chrom-pos-ref-alt + """ + # pylint: disable=too-many-locals,too-many-branches,too-many-statements dataset, ds_version = utils.parse_dataset(dataset, ds_version) - ret = {'variant':{}} + ret = {'variant': {}} # Variant - v = variant.split('-') - if len(v) != 4: + split_var = variant.split('-') + if len(split_var) != 4: logging.error('GetVariant: unable to parse variant ({})'.format(variant)) self.send_error(status_code=400, reason=f'Unable to parse variant {variant}') try: - v[1] = int(v[1]) + split_var[1] = int(split_var[1]) except ValueError: logging.error('GetVariant: position not an integer ({})'.format(variant)) - self.send_error(status_code=400, reason=f'Position is not an integer in variant {variant}') + self.send_error(status_code=400, + reason=f'Position is not an integer in variant {variant}') return orig_variant = variant try: - variant = lookups.get_variant(dataset, v[1], v[0], v[2], v[3], ds_version) + variant = lookups.get_variant(dataset, split_var[1], split_var[0], + split_var[2], split_var[3], ds_version) except error.NotFoundError as err: logging.error('Variant not found ({})'.format(orig_variant)) self.send_error(status_code=404, reason=str(err)) @@ -301,8 +309,8 @@ def get(self, dataset:str, variant:str, ds_version:str=None): # Just get the information we need for item in ["variant_id", "chrom", "pos", "ref", "alt", "rsid", "allele_num", - "allele_freq", "allele_count", "orig_alt_alleles", "site_quality", "quality_metrics", - "transcripts", "genes"]: + "allele_freq", "allele_count", "orig_alt_alleles", "site_quality", + "quality_metrics", "transcripts", "genes"]: ret['variant'][item] = variant[item] ret['variant']['filter'] = variant['filter_string'] @@ -311,7 +319,8 @@ def get(self, dataset:str, variant:str, ds_version:str=None): ret['variant']['consequences'] = [] if 'vep_annotations' in variant: utils.add_consequence_to_variant(variant) - variant['vep_annotations'] = utils.remove_extraneous_vep_annotations(variant['vep_annotations']) + variant['vep_annotations'] = \ + utils.remove_extraneous_vep_annotations(variant['vep_annotations']) # Adds major_consequence variant['vep_annotations'] = utils.order_vep_by_csq(variant['vep_annotations']) ret['variant']['annotations'] = {} @@ -319,21 +328,22 @@ def get(self, dataset:str, variant:str, ds_version:str=None): annotation['HGVS'] = utils.get_proper_hgvs(annotation) # Add consequence type to the annotations if it doesn't exist - consequence_type = annotation['Consequence'].split('&')[0] \ - .replace("_variant", "") \ - .replace('_prime_', '\'') \ - .replace('_', ' ') + consequence_type = (annotation['Consequence'].split('&')[0] + .replace("_variant", "") + .replace('_prime_', '\'') + .replace('_', ' ')) if consequence_type not in ret['variant']['annotations']: - ret['variant']['annotations'][consequence_type] = {'gene': {'name':annotation['SYMBOL'], - 'id':annotation['Gene']}, - 'transcripts':[]} + ret['variant']['annotations'][consequence_type] = \ + {'gene': {'name': annotation['SYMBOL'], + 'id': annotation['Gene']}, + 'transcripts': []} ret['variant']['annotations'][consequence_type]['transcripts'] += \ - [{'id': annotation['Feature'], - 'sift': annotation['SIFT'].rstrip("()0123456789"), - 'polyphen': annotation['PolyPhen'].rstrip("()0123456789"), - 'canonical': annotation['CANONICAL'], - 'modification': annotation['HGVSp'].split(":")[1] if ':' in annotation['HGVSp'] else None}] + [{'id': annotation['Feature'], + 'sift': annotation['SIFT'].rstrip("()0123456789"), + 'polyphen': annotation['PolyPhen'].rstrip("()0123456789"), + 'canonical': annotation['CANONICAL'], + 'modification': annotation['HGVSp'].split(":")[1] if ':' in annotation['HGVSp'] else None}] # pylint: disable=line-too-long # Dataset frequencies. # This is reported per variable in the database data, with dataset @@ -342,24 +352,32 @@ def get(self, dataset:str, variant:str, ds_version:str=None): # get the variant for other datasets with the same reference_set curr_dsv = db.get_dataset_version(dataset, ds_version) - dsvs = [db.get_dataset_version(dset.short_name) for dset in db.Dataset.select() if dset.short_name != dataset] + dsvs = [db.get_dataset_version(dset.short_name) for dset in db.Dataset.select() + if dset.short_name != dataset] + # if the only available version is not released yet + dsvs = list(filter(lambda dsv: dsv, dsvs)) + logging.error(dsvs) dsvs = [dsv for dsv in dsvs if dsv.reference_set == curr_dsv.reference_set] dsv_groups = [(curr_dsv, variant)] for dsv in dsvs: try: - hit = lookups.get_variant(dsv.dataset.short_name, v[1], v[0], v[2], v[3], dsv.version) + hit = lookups.get_variant(dsv.dataset.short_name, split_var[1], split_var[0], + split_var[2], split_var[3], dsv.version) except error.NotFoundError: continue dsv_groups.append((dsv, hit)) - frequencies = {'headers':[['Dataset','pop'], - ['Allele Count','acs'], - ['Allele Number', 'ans'], - ['Number of Homozygotes', 'homs'], - ['Allele Frequency', 'freq']], - 'datasets':{}, - 'total':{}} - term_map = {'allele_num':'ans', 'allele_count':'acs', 'allele_freq':'freq', 'hom_count':'homs'} + frequencies = {'headers': [['Dataset', 'pop'], + ['Allele Count', 'acs'], + ['Allele Number', 'ans'], + ['Number of Homozygotes', 'homs'], + ['Allele Frequency', 'freq']], + 'datasets': {}, + 'total': {}} + term_map = {'allele_num': 'ans', + 'allele_count': 'acs', + 'allele_freq': 'freq', + 'hom_count': 'homs'} for dsv_group in dsv_groups: ds_name = dsv_group[0].dataset.short_name @@ -376,7 +394,8 @@ def get(self, dataset:str, variant:str, ds_version:str=None): frequencies['total'][term_map[item]] += dsv_group[1][item] if 'freq' in frequencies['total']: - frequencies['total']['freq'] = frequencies['total']['acs']/frequencies['total']['ans'] + frequencies['total']['freq'] = \ + frequencies['total']['acs']/frequencies['total']['ans'] ret['variant']['pop_freq'] = frequencies self.finish(ret) @@ -385,7 +404,7 @@ def get(self, dataset:str, variant:str, ds_version:str=None): class GetVariants(handlers.UnsafeHandler): """Retrieve variants.""" - def get(self, dataset:str, datatype:str, item:str, ds_version:str=None): + def get(self, dataset: str, datatype: str, item: str, ds_version: str = None): """ Retrieve variants. @@ -393,6 +412,7 @@ def get(self, dataset:str, datatype:str, item:str, ds_version:str=None): dataset (str): short name of the dataset datatype (str): gene, region, or transcript item (str): item to query + """ dataset, ds_version = utils.parse_dataset(dataset, ds_version) try: @@ -416,13 +436,14 @@ def get(self, dataset:str, datatype:str, item:str, ds_version:str=None): class Search(handlers.UnsafeHandler): """Perform a search for the wanted object.""" - def get(self, dataset:str, query:str, ds_version:str=None): + def get(self, dataset: str, query: str, ds_version: str = None): """ Perform a search for the wanted object. Args: dataset (str): short name of the dataset query (str): search query + """ dataset, ds_version = utils.parse_dataset(dataset, ds_version) ret = {"dataset": dataset, "value": None, "type": None} diff --git a/backend/modules/browser/error.py b/backend/modules/browser/error.py index 606bb5c2e..fb7766098 100644 --- a/backend/modules/browser/error.py +++ b/backend/modules/browser/error.py @@ -1,11 +1,10 @@ class NotFoundError(Exception): """The query returned nothing from the database.""" - pass + class ParsingError(Exception): """Failed to parse the request.""" - pass + class MalformedRequest(Exception): """Bad request (e.g. too large region).""" - pass diff --git a/backend/modules/browser/lookups.py b/backend/modules/browser/lookups.py index 3a518cb7f..d538fab57 100644 --- a/backend/modules/browser/lookups.py +++ b/backend/modules/browser/lookups.py @@ -12,7 +12,7 @@ REGION_REGEX = re.compile(r'^\s*(\d+|X|Y|M|MT)\s*([-:]?)\s*(\d*)-?([\dACTG]*)-?([ACTG]*)') -def autocomplete(dataset:str, query:str, ds_version:str=None): +def autocomplete(dataset: str, query: str, ds_version: str = None) -> list: """ Provide autocomplete suggestions based on the query. @@ -27,16 +27,16 @@ def autocomplete(dataset:str, query:str, ds_version:str=None): """ try: ref_set = db.get_dataset_version(dataset, ds_version).reference_set - except AttributeError: - raise error.NotFoundError(f'Reference set not found for dataset {dataset}.') + except AttributeError as err: + raise error.NotFoundError(f'Reference set not found for dataset {dataset}.') from err query = (db.Gene.select(db.Gene.name) .where(((db.Gene.name.startswith(query)) & - (db.Gene.reference_set == ref_set)))) + (db.Gene.reference_set == ref_set)))) gene_names = [str(gene.name) for gene in query] return gene_names -def get_awesomebar_result(dataset:str, query:str, ds_version:str=None): +def get_awesomebar_result(dataset: str, query: str, ds_version: str = None) -> tuple: """ Parse the search input. @@ -69,6 +69,7 @@ def get_awesomebar_result(dataset:str, query:str, ds_version:str=None): tuple: (datatype, identifier) """ + # pylint: disable=too-many-return-statements,too-many-branches query = query.strip() # Parse Variant types @@ -84,35 +85,32 @@ def get_awesomebar_result(dataset:str, query:str, ds_version:str=None): # Gene try: gene = get_gene_by_name(dataset, query) + return 'gene', gene['gene_id'] except error.NotFoundError: pass - else: - return 'gene', gene['gene_id'] + # Capital letters for all other queries query = query.upper() try: gene = get_gene_by_name(dataset, query) + return 'gene', gene['gene_id'] except error.NotFoundError: pass - else: - return 'gene', gene['gene_id'] # Ensembl formatted queries if query.startswith('ENS'): # Gene try: gene = get_gene(dataset, query) + return 'gene', gene['gene_id'] except error.NotFoundError: pass - else: - return 'gene', gene['gene_id'] # Transcript try: transcript = get_transcript(dataset, query) + return 'transcript', transcript['transcript_id'] except error.NotFoundError: pass - else: - return 'transcript', transcript['transcript_id'] # Region and variant queries query = query[3:] if query.startswith('CHR') else query @@ -122,13 +120,14 @@ def get_awesomebar_result(dataset:str, query:str, ds_version:str=None): target = match.group(0) target_type = 'region' if match.group(2) == ":": - target = target.replace(":","-") + target = target.replace(":", "-") if match.group(5) and set(match.group(4)).issubset(set("ACGT")): target_type = 'variant' try: - get_raw_variant(dataset, match.group(3), match.group(1), match.group(4), match.group(5), ds_version) - except error.NotFoundError as err: + get_raw_variant(dataset, int(match.group(3)), match.group(1), + match.group(4), match.group(5), ds_version) + except error.NotFoundError: target_type = 'not_found' return target_type, target @@ -136,7 +135,8 @@ def get_awesomebar_result(dataset:str, query:str, ds_version:str=None): return 'not_found', query -def get_coverage_for_bases(dataset:str, chrom:str, start_pos:int, end_pos:int=None, ds_version:str=None): +def get_coverage_for_bases(dataset: str, chrom: str, start_pos: int, + end_pos: int = None, ds_version: str = None) -> list: """ Get the coverage for the list of bases given by start_pos->end_pos, inclusive. @@ -168,7 +168,8 @@ def get_coverage_for_bases(dataset:str, chrom:str, start_pos:int, end_pos:int=No return coverage -def get_coverage_for_transcript(dataset:str, chrom:str, start_pos:int, end_pos:int=None, ds_version:str=None): +def get_coverage_for_transcript(dataset: str, chrom: str, start_pos: int, + end_pos: int = None, ds_version: str = None) -> list: """ Get the coverage for the list of bases given by start_pos->end_pos, inclusive. @@ -194,7 +195,7 @@ def get_coverage_for_transcript(dataset:str, chrom:str, start_pos:int, end_pos:i return covered -def get_exons_in_transcript(dataset:str, transcript_id:str, ds_version=None): +def get_exons_in_transcript(dataset: str, transcript_id: str, ds_version: str = None) -> list: """ Retrieve exons associated with the given transcript id. @@ -210,7 +211,8 @@ def get_exons_in_transcript(dataset:str, transcript_id:str, ds_version=None): try: ref_set = db.get_dataset_version(dataset, ds_version).reference_set except AttributeError: - logging.info('get_exons_in_transcript({}, {}): unable to find dataset dbid'.format(dataset, transcript_id)) + logging.info(f'get_exons_in_transcript({dataset}, ' + + f'{transcript_id}): unable to find dataset dbid') raise error.NotFoundError(f'Reference set not found for dataset {dataset}.') try: @@ -220,19 +222,22 @@ def get_exons_in_transcript(dataset:str, transcript_id:str, ds_version=None): .where((db.Transcript.transcript_id == transcript_id) & (db.Gene.reference_set == ref_set)) .get()) - except db.Transcript.DoesNotExist: - logging.info('get_exons_in_transcript({}, {}): unable to retrieve transcript'.format(dataset, transcript_id)) - raise error.NotFoundError(f'Transcript {transcript_id} not found in reference data.') + except db.Transcript.DoesNotExist as err: + logging.info('get_exons_in_transcript({dataset}, {transcript_id}): ' + + 'unable to retrieve transcript') + raise error.NotFoundError(f'Transcript {transcript_id} not found in reference.') from err wanted_types = ('CDS', 'UTR', 'exon') - features = sorted(list(db.Feature.select().where((db.Feature.transcript == transcript) & - (db.Feature.feature_type in wanted_types)).dicts()), + features = sorted(list(db.Feature.select() + .where((db.Feature.transcript == transcript) & + (db.Feature.feature_type in wanted_types)) + .dicts()), key=lambda k: k['start']) if not features: - raise error.NotFoundError(f'No features found for transcript {transcript_id} in reference data.') + raise error.NotFoundError(f'No features found for transcript {transcript_id} in reference.') return features -def get_gene(dataset:str, gene_id:str, ds_version:str=None): +def get_gene(dataset: str, gene_id: str, ds_version: str = None) -> dict: """ Retrieve gene by gene id. @@ -247,17 +252,17 @@ def get_gene(dataset:str, gene_id:str, ds_version:str=None): """ try: ref_set = db.get_dataset_version(dataset, ds_version).reference_set - except AttributeError: - raise error.NotFoundError(f'Reference set not found for dataset {dataset}.') + except AttributeError as err: + raise error.NotFoundError(f'Reference set not found for dataset {dataset}.') from err try: return db.Gene.select().where((db.Gene.gene_id == gene_id) & (db.Gene.reference_set == ref_set)).dicts().get() - except db.Gene.DoesNotExist: - raise error.NotFoundError(f'Gene {gene_id} not found in reference data.') + except db.Gene.DoesNotExist as err: + raise error.NotFoundError(f'Gene {gene_id} not found in reference data.') from err -def get_gene_by_dbid(gene_dbid:str): +def get_gene_by_dbid(gene_dbid: str) -> dict: """ Retrieve gene by gene database id. @@ -276,7 +281,7 @@ def get_gene_by_dbid(gene_dbid:str): return {} -def get_gene_by_name(dataset:str, gene_name:str, ds_version=None): +def get_gene_by_name(dataset: str, gene_name: str, ds_version: str = None) -> dict: """ Retrieve gene by gene_name. @@ -291,13 +296,13 @@ def get_gene_by_name(dataset:str, gene_name:str, ds_version=None): """ try: ref_set = db.get_dataset_version(dataset, ds_version).reference_set - except AttributeError: - raise error.NotFoundError(f'Reference set not found for dataset {dataset}.') + except AttributeError as err: + raise error.NotFoundError(f'Reference set not found for dataset {dataset}.') from err try: return (db.Gene.select() .where((db.Gene.reference_set == ref_set) & - (db.Gene.name==gene_name)) + (db.Gene.name == gene_name)) .dicts() .get()) except db.Gene.DoesNotExist: @@ -308,12 +313,13 @@ def get_gene_by_name(dataset:str, gene_name:str, ds_version=None): (db.Gene.reference_set == ref_set)) .dicts() .get()) - except db.GeneOtherNames.DoesNotExist: - logging.info('get_gene_by_name({}, {}): unable to retrieve gene'.format(dataset, gene_name)) - raise error.NotFoundError(f'Gene {gene_name} not found in reference data') + except db.GeneOtherNames.DoesNotExist as err: + logging.info(f'get_gene_by_name({dataset}, {gene_name}): unable to retrieve gene') + raise error.NotFoundError(f'Gene {gene_name} not found in reference data') from err -def get_genes_in_region(dataset:str, chrom:str, start_pos:int, stop_pos:int, ds_version:str=None): +def get_genes_in_region(dataset: str, chrom: str, start_pos: int, + stop_pos: int, ds_version: str = None) -> dict: """ Retrieve genes located within a region. @@ -330,8 +336,8 @@ def get_genes_in_region(dataset:str, chrom:str, start_pos:int, stop_pos:int, ds_ """ try: ref_set = db.get_dataset_version(dataset, ds_version).reference_set - except AttributeError: - raise error.NotFoundError(f'Reference set not found for dataset {dataset}.') + except AttributeError as err: + raise error.NotFoundError(f'Reference set not found for dataset {dataset}.') from err genes = db.Gene.select().where((db.Gene.reference_set == ref_set) & (db.Gene.start <= stop_pos) & @@ -340,7 +346,8 @@ def get_genes_in_region(dataset:str, chrom:str, start_pos:int, stop_pos:int, ds_ return genes -def get_raw_variant(dataset:str, pos:int, chrom:str, ref:str, alt:str, ds_version:str=None): +def get_raw_variant(dataset: str, pos: int, chrom: str, ref: str, # pylint: disable=too-many-arguments + alt: str, ds_version: str = None) -> dict: """ Retrieve variant by position and change. @@ -381,13 +388,13 @@ def get_raw_variant(dataset:str, pos:int, chrom:str, ref:str, alt:str, ds_versio .where(db.VariantTranscripts.variant == variant['id']) .dicts()] return variant - except db.Variant.DoesNotExist: + except db.Variant.DoesNotExist as err: logging.info('get_raw_variant({}, {}, {}, {}, {}, {}): unable to retrieve variant' .format(dataset, pos, chrom, ref, alt, dataset_version.id)) - raise error.NotFoundError(f'Variant {chrom}-{pos}-{ref}-{alt} not found') + raise error.NotFoundError(f'Variant {chrom}-{pos}-{ref}-{alt} not found') from err -def get_transcript(dataset:str, transcript_id:str, ds_version:str=None): +def get_transcript(dataset: str, transcript_id: str, ds_version: str = None) -> dict: """ Retrieve transcript by transcript id. @@ -404,8 +411,8 @@ def get_transcript(dataset:str, transcript_id:str, ds_version:str=None): """ try: ref_set = db.get_dataset_version(dataset, ds_version).reference_set - except AttributeError: - raise error.NotFoundError(f'Reference set not found for dataset {dataset}.') + except AttributeError as err: + raise error.NotFoundError(f'Reference set not found for dataset {dataset}.') from err try: transcript = (db.Transcript .select(db.Transcript, db.Gene.gene_id) @@ -416,12 +423,12 @@ def get_transcript(dataset:str, transcript_id:str, ds_version:str=None): .get()) transcript['exons'] = get_exons_in_transcript(dataset, transcript_id) return transcript - except db.Transcript.DoesNotExist: - logging.info('get_transcript({}, {}): unable to retrieve transcript'.format(dataset, transcript_id)) - raise error.NotFoundError(f'Transcript {transcript_id} not found in reference data') + except db.Transcript.DoesNotExist as err: + logging.info(f'get_transcript({dataset}, {transcript_id}): unable to retrieve transcript') + raise error.NotFoundError(f'Transcript {transcript_id} not found in reference') from err -def get_transcripts_in_gene(dataset:str, gene_id:str, ds_version:str=None): +def get_transcripts_in_gene(dataset: str, gene_id: str, ds_version: str = None) -> list: """ Get the transcripts associated with a gene. @@ -436,21 +443,26 @@ def get_transcripts_in_gene(dataset:str, gene_id:str, ds_version:str=None): """ try: ref_set = db.get_dataset_version(dataset, ds_version).reference_set - except AttributeError: - logging.warning('get_transcripts_in_gene({}, {}): unable to get referenceset dbid'.format(dataset, gene_id)) - raise error.NotFoundError(f'Reference set not found for dataset {dataset}.') + except AttributeError as err: + logging.warning(f'get_transcripts_in_gene({dataset}, {gene_id}): unable to get ref dbid') + raise error.NotFoundError(f'Reference set not found for dataset {dataset}.') from err try: - gene = db.Gene.select().where((db.Gene.reference_set == ref_set) & - (db.Gene.gene_id == gene_id)).dicts().get() - except db.Gene.DoesNotExist: - logging.info('get_transcripts_in_gene({}, {}): unable to retrieve gene'.format(dataset, gene_id)) - raise error.NotFoundError(f'Gene {gene_id} not found in reference data') + gene = (db.Gene.select() + .where((db.Gene.reference_set == ref_set) & + (db.Gene.gene_id == gene_id)) + .dicts() + .get()) + except db.Gene.DoesNotExist as err: + logging.info('get_transcripts_in_gene({dataset}, {gene_id}): unable to retrieve gene') + raise error.NotFoundError(f'Gene {gene_id} not found in reference data') from err - return [transcript for transcript in db.Transcript.select().where(db.Transcript.gene == gene['id']).dicts()] + return [transcript for transcript in (db.Transcript.select() + .where(db.Transcript.gene == gene['id']) + .dicts())] -def get_transcripts_in_gene_by_dbid(gene_dbid:int): +def get_transcripts_in_gene_by_dbid(gene_dbid: int) -> list: """ Get the transcripts associated with a gene. @@ -461,10 +473,13 @@ def get_transcripts_in_gene_by_dbid(gene_dbid:int): list: transcripts (dict) associated with the gene; empty if no hits """ - return [transcript for transcript in db.Transcript.select().where(db.Transcript.gene == gene_dbid).dicts()] + return [transcript for transcript in (db.Transcript.select() + .where(db.Transcript.gene == gene_dbid) + .dicts())] -def get_variant(dataset:str, pos:int, chrom:str, ref:str, alt:str, ds_version:str=None): +def get_variant(dataset: str, pos: int, chrom: str, ref: str, # pylint: disable=too-many-arguments + alt: str, ds_version: str = None) -> dict: """ Retrieve variant by position and change. @@ -482,12 +497,12 @@ def get_variant(dataset:str, pos:int, chrom:str, ref:str, alt:str, ds_version:st """ variant = get_raw_variant(dataset, pos, chrom, ref, alt, ds_version) variant = get_raw_variant(dataset, pos, chrom, ref, alt, ds_version) - if variant and 'rsid' in variant and variant['rsid'] and not str(variant['rsid']).startswith('rs'): + if variant and variant.get('rsid') and not str(variant['rsid']).startswith('rs'): variant['rsid'] = 'rs{}'.format(variant['rsid']) return variant -def get_variants_by_rsid(dataset:str, rsid:str, ds_version:str=None): +def get_variants_by_rsid(dataset: str, rsid: str, ds_version: str = None) -> list: """ Retrieve variants by their associated rsid. @@ -505,17 +520,18 @@ def get_variants_by_rsid(dataset:str, rsid:str, ds_version:str=None): raise error.NotFoundError(f'Unable to find the dataset version in the database') if not rsid.startswith('rs'): - logging.error('get_variants_by_rsid({}, {}): rsid not starting with rs'.format(dataset, rsid)) + logging.error('get_variants_by_rsid({dataset}, {rsid}): rsid not starting with rs') raise error.ParsingError('rsid not starting with rs') try: - rsid = int(rsid.lstrip('rs')) - except ValueError: + int_rsid = int(rsid.lstrip('rs')) + except ValueError as err: logging.error('get_variants_by_rsid({}, {}): not an integer after rs'.format(dataset, rsid)) - raise error.ParsingError('Not an integer after rs') + raise error.ParsingError('Not an integer after rs') from err + variants = (db.Variant .select() - .where((db.Variant.rsid == rsid) & + .where((db.Variant.rsid == int_rsid) & (db.Variant.dataset_version == dataset_version)) .dicts()) @@ -524,7 +540,7 @@ def get_variants_by_rsid(dataset:str, rsid:str, ds_version:str=None): return variants -def get_variants_in_gene(dataset:str, gene_id:str, ds_version:str=None): +def get_variants_in_gene(dataset: str, gene_id: str, ds_version: str = None) -> list: """ Retrieve variants present inside a gene. @@ -544,16 +560,15 @@ def get_variants_in_gene(dataset:str, gene_id:str, ds_version:str=None): if not gene: raise error.NotFoundError(f'Gene {gene_id} not found in reference data') - variants = [variant for variant in db.Variant.select() - .join(db.VariantGenes) - .where((db.VariantGenes.gene == gene['id']) & - (db.Variant.dataset_version == dataset_version)).dicts()] - ##### remove when db is fixed + variants = [variant for variant in (db.Variant.select() + .join(db.VariantGenes) + .where((db.VariantGenes.gene == gene['id']) & + (db.Variant.dataset_version == dataset_version)) + .dicts())] for variant in variants: if not variant['hom_count']: variant['hom_count'] = 0 variant['filter'] = variant['filter_string'] - ##### for variant in variants: if variant['rsid']: @@ -561,7 +576,8 @@ def get_variants_in_gene(dataset:str, gene_id:str, ds_version:str=None): return variants -def get_variants_in_region(dataset:str, chrom:str, start_pos:int, end_pos:int, ds_version:str=None): +def get_variants_in_region(dataset: str, chrom: str, start_pos: int, + end_pos: int, ds_version: str = None) -> list: """ Variants that overlap a region. @@ -589,12 +605,10 @@ def get_variants_in_region(dataset:str, chrom:str, start_pos:int, end_pos:int, d variants = [variant for variant in query] - ##### remove when db is fixed for variant in variants: if not variant['hom_count']: variant['hom_count'] = 0 variant['filter'] = variant['filter_string'] - ##### for variant in variants: if variant['rsid']: @@ -602,7 +616,7 @@ def get_variants_in_region(dataset:str, chrom:str, start_pos:int, end_pos:int, d return variants -def get_variants_in_transcript(dataset:str, transcript_id:str, ds_version:str=None): +def get_variants_in_transcript(dataset: str, transcript_id: str, ds_version: str = None) -> list: """ Retrieve variants inside a transcript. @@ -612,7 +626,7 @@ def get_variants_in_transcript(dataset:str, transcript_id:str, ds_version:str=No ds_version (str): version of the dataset Returns: - dict: values for the variant; None if not found + list: values for the variant; None if not found """ dataset_version = db.get_dataset_version(dataset, ds_version) @@ -629,15 +643,14 @@ def get_variants_in_transcript(dataset:str, transcript_id:str, ds_version:str=No (db.Variant.dataset_version == dataset_version)) .dicts()] - ##### remove when db is fixed for variant in variants: if not variant['hom_count']: variant['hom_count'] = 0 variant['filter'] = variant['filter_string'] - ##### for variant in variants: - variant['vep_annotations'] = [anno for anno in variant['vep_annotations'] if anno['Feature'] == transcript_id] + variant['vep_annotations'] = [anno for anno in variant['vep_annotations'] + if anno['Feature'] == transcript_id] if variant['rsid']: variant['rsid'] = 'rs{}'.format(variant['rsid']) return variants diff --git a/backend/modules/browser/route.py b/backend/modules/browser/route.py index 222309535..6e011009b 100755 --- a/backend/modules/browser/route.py +++ b/backend/modules/browser/route.py @@ -1,14 +1,15 @@ from . import browser_handlers as handlers +# pylint: disable=line-too-long + # Browser links -routes = [(r"/api/dataset/(?P[^/]+)/(?:version/(?P[^/]+)/)?browser/gene/(?P[^/]+)" , handlers.GetGene), - (r"/api/dataset/(?P[^/]+)/(?:version/(?P[^/]+)/)?browser/region/(?P[^\/]+)", handlers.GetRegion), - (r"/api/dataset/(?P[^/]+)/(?:version/(?P[^/]+)/)?browser/transcript/(?P[^/]+)", handlers.GetTranscript), - (r"/api/dataset/(?P[^/]+)/(?:version/(?P[^/]+)/)?browser/variant/(?P[^/]+)", handlers.GetVariant), - (r"/api/dataset/(?P[^/]+)/(?:version/(?P[^/]+)/)?browser/variants/(?P[^/]+)/(?P[^/]+)", handlers.GetVariants), - (r"/api/dataset/(?P[^/]+)/(?:version/(?P[^/]+)/)?browser/coverage/(?P[^/]+)/(?P[^/]+)", handlers.GetCoverage), - (r"/api/dataset/(?P[^/]+)/(?:version/(?P[^/]+)/)?browser/coverage_pos/(?P[^/]+)/(?P[^/]+)", handlers.GetCoveragePos), - (r"/api/dataset/(?P[^/]+)/(?:version/(?P[^/]+)/)?browser/autocomplete/(?P[^/]+)", handlers.Autocomplete), - (r"/api/dataset/(?P[^/]+)/(?:version/(?P[^/]+)/)?browser/search/(?P[^/]+)", handlers.Search), - (r"/api/dataset/(?P[^/]+)/(?:version/(?P[^/]+)/)?browser/download/(?P[^/]+)/(?P[^/]+)(?:/filter/(?P[^/]+))?", handlers.Download), - ] +routes = [(r"/api/dataset/(?P[^/]+)/(?:version/(?P[^/]+)/)?browser/gene/(?P[^/]+)", handlers.GetGene), + (r"/api/dataset/(?P[^/]+)/(?:version/(?P[^/]+)/)?browser/region/(?P[^\/]+)", handlers.GetRegion), + (r"/api/dataset/(?P[^/]+)/(?:version/(?P[^/]+)/)?browser/transcript/(?P[^/]+)", handlers.GetTranscript), + (r"/api/dataset/(?P[^/]+)/(?:version/(?P[^/]+)/)?browser/variant/(?P[^/]+)", handlers.GetVariant), + (r"/api/dataset/(?P[^/]+)/(?:version/(?P[^/]+)/)?browser/variants/(?P[^/]+)/(?P[^/]+)", handlers.GetVariants), + (r"/api/dataset/(?P[^/]+)/(?:version/(?P[^/]+)/)?browser/coverage/(?P[^/]+)/(?P[^/]+)", handlers.GetCoverage), + (r"/api/dataset/(?P[^/]+)/(?:version/(?P[^/]+)/)?browser/coverage_pos/(?P[^/]+)/(?P[^/]+)", handlers.GetCoveragePos), + (r"/api/dataset/(?P[^/]+)/(?:version/(?P[^/]+)/)?browser/autocomplete/(?P[^/]+)", handlers.Autocomplete), + (r"/api/dataset/(?P[^/]+)/(?:version/(?P[^/]+)/)?browser/search/(?P[^/]+)", handlers.Search), + (r"/api/dataset/(?P[^/]+)/(?:version/(?P[^/]+)/)?browser/download/(?P[^/]+)/(?P[^/]+)(?:/filter/(?P[^/]+))?", handlers.Download)] diff --git a/backend/modules/browser/tests/test_browser_handlers.py b/backend/modules/browser/tests/test_browser_handlers.py index b69797afb..2657323de 100644 --- a/backend/modules/browser/tests/test_browser_handlers.py +++ b/backend/modules/browser/tests/test_browser_handlers.py @@ -1,10 +1,13 @@ """ Test the browser handlers """ -import requests import json -BASE_URL="http://localhost:4000" +import requests + +BASE_URL = "http://localhost:4000" + +# pylint: disable=line-too-long def test_get_autocomplete(): """ @@ -28,21 +31,24 @@ def test_download(): data_type = 'transcript' data_item = 'ENST00000438441' response = requests.get('{}/api/dataset/{}/browser/download/{}/{}'.format(BASE_URL, dataset, data_type, data_item)) - assert len(response.text.split('\n')) == 180 # header + 178 + \n + assert len(response.text.split('\n')) == 180 # header + 178 + \n response = requests.get('{}/api/dataset/{}/browser/download/{}/{}/filter/all~false'.format(BASE_URL, dataset, data_type, data_item)) - import logging - logging.error(response.text.split('\n')) assert len(response.text.split('\n')) == 8 response = requests.get('{}/api/dataset/{}/browser/download/{}/{}/filter/all~true'.format(BASE_URL, dataset, data_type, data_item)) assert len(response.text.split('\n')) == 180 response = requests.get('{}/api/dataset/{}/browser/download/{}/{}/filter/mislof~true'.format(BASE_URL, dataset, data_type, data_item)) assert len(response.text.split('\n')) == 2 + filename = f'{dataset}_{data_type}_{data_item}.csv' + assert response.headers['content-disposition'] == f'attachment; filename={filename}' + data_type = 'region' data_item = '22-29450622-29465622' response = requests.get('{}/api/dataset/{}/browser/download/{}/{}/filter/mislof~false'.format(BASE_URL, dataset, data_type, data_item)) assert len(response.text.split('\n')) == 3 response = requests.get('{}/api/dataset/{}/browser/download/{}/{}/filter/lof~false'.format(BASE_URL, dataset, data_type, data_item)) assert len(response.text.split('\n')) == 3 + filename = f'{dataset}_{data_type}_{data_item}.csv' + assert response.headers['content-disposition'] == f'attachment; filename={filename}' def test_get_coverage(): @@ -78,6 +84,22 @@ def test_get_coverage_pos(): assert cov_pos['stop'] == 100101 assert cov_pos['chrom'] == '22' + data_type = 'region' + data_item = '22-100001-200101' + response = requests.get('{}/api/dataset/{}/browser/coverage_pos/{}/{}'.format(BASE_URL, dataset, data_type, data_item)) + assert response.status_code == 400 + + data_type = 'region' + data_item = '22-1-11-101' + response = requests.get('{}/api/dataset/{}/browser/coverage_pos/{}/{}'.format(BASE_URL, dataset, data_type, data_item)) + assert response.status_code == 400 + + dataset = 'SweGen' + data_type = 'transcript' + data_item = 'BAD_TRANSCRIPT' + response = requests.get('{}/api/dataset/{}/browser/coverage_pos/{}/{}'.format(BASE_URL, dataset, data_type, data_item)) + assert response.status_code == 404 + def test_get_gene(): """ @@ -194,6 +216,10 @@ def test_get_variant(): response = requests.get('{}/api/dataset/{}/browser/variant/{}'.format(BASE_URL, dataset, variant_id)) assert response.status_code == 400 + variant_id = '1-2-3-4-5-6' + response = requests.get('{}/api/dataset/{}/browser/variant/{}'.format(BASE_URL, dataset, variant_id)) + assert response.status_code == 400 + def test_get_variants(): """ diff --git a/backend/modules/browser/tests/test_lookups.py b/backend/modules/browser/tests/test_lookups.py index 6de69d606..245f71e01 100644 --- a/backend/modules/browser/tests/test_lookups.py +++ b/backend/modules/browser/tests/test_lookups.py @@ -14,7 +14,7 @@ def test_autocomplete(): """ res = lookups.autocomplete('SweGen', 'PA') expected = set(["PABPC1P9", "PACSIN2", "PANX2", "PARP4P3", - "PARVB", "PARVG", "PATZ1", "PAXBP1", "PAXBP1-AS1"]) + "PARVB", "PARVG", "PATZ1", "PAXBP1", "PAXBP1-AS1"]) assert set(res) == expected with pytest.raises(error.NotFoundError): res = lookups.autocomplete('Bad_dataset', 'PA') @@ -54,7 +54,7 @@ def test_get_coverage_for_bases(): coverage = lookups.get_coverage_for_bases('SweGen', '22', 46546423, 46549652) assert len(coverage) == 323 expected = {'chrom': '22', 'coverage': [1.0, 1.0, 0.993, 0.91, 0.697, 0.426, 0.2, 0.009, 0.0], - 'dataset_version': 4, 'mean': 24.94, 'median': 24.0, 'pos': 46546430} + 'dataset_version': 4, 'mean': 24.94, 'median': 24.0, 'pos': 46546430} for val in expected: assert coverage[0][val] == expected[val] @@ -175,7 +175,7 @@ def test_get_gene_by_dbid(): assert not result -def test_get_gene_by_name(caplog): +def test_get_gene_by_name(): """ Test get_gene_by_name() """ diff --git a/backend/modules/browser/tests/test_utils.py b/backend/modules/browser/tests/test_utils.py index 83361475e..3c7a79787 100644 --- a/backend/modules/browser/tests/test_utils.py +++ b/backend/modules/browser/tests/test_utils.py @@ -89,7 +89,7 @@ def test_get_coverage(): # no coverage found with pytest.raises(error.NotFoundError): - utils.get_coverage('BAD_SET', 'transcript', 'ENST00000438441')['coverage'] + res = utils.get_coverage('BAD_SET', 'transcript', 'ENST00000438441')['coverage'] with pytest.raises(error.MalformedRequest): res = utils.get_coverage('SweGen', 'region', '22-1-1000000') @@ -127,31 +127,31 @@ def test_get_coverage_pos(): utils.get_coverage_pos('SweGen', 'region', '1-1-10000000') - def test_data_structures(): """ Test the constants """ - assert len(utils.CSQ_ORDER) == len(set(utils.CSQ_ORDER)) # No duplicates - assert all(csq == utils.REV_CSQ_ORDER_DICT[utils.CSQ_ORDER_DICT[csq]] for csq in utils.CSQ_ORDER) + assert len(utils.CSQ_ORDER) == len(set(utils.CSQ_ORDER)) # No duplicates + assert all(csq == utils.REV_CSQ_ORDER_DICT[utils.CSQ_ORDER_DICT[csq]] + for csq in utils.CSQ_ORDER) def test_get_flags_from_variant(): """ Test get_flags_from_variant() """ - fake_variant = {'vep_annotations':[{'LoF': 'LC', 'LoF_flags': 'something'}, - {'LoF': '', 'LoF_flags': ''}, - {'LoF': 'LC', 'LoF_flags': 'something'}]} + fake_variant = {'vep_annotations': [{'LoF': 'LC', 'LoF_flags': 'something'}, + {'LoF': '', 'LoF_flags': ''}, + {'LoF': 'LC', 'LoF_flags': 'something'}]} flags = utils.get_flags_from_variant(fake_variant) assert flags == ['LC LoF', 'LoF flag'] - fake_variant = {'vep_annotations':[{'LoF': 'LC', 'LoF_flags': 'something'}, - {'LoF': 'HC', 'LoF_flags': 'something'}]} + fake_variant = {'vep_annotations': [{'LoF': 'LC', 'LoF_flags': 'something'}, + {'LoF': 'HC', 'LoF_flags': 'something'}]} flags = utils.get_flags_from_variant(fake_variant) assert flags == ['LoF', 'LoF flag'] - fake_variant = {'mnps': 'no idea', 'vep_annotations':[]} + fake_variant = {'mnps': 'no idea', 'vep_annotations': []} flags = utils.get_flags_from_variant(fake_variant) assert flags == ['MNP'] @@ -212,7 +212,6 @@ def test_get_variant_list(): res = utils.get_variant_list('SweGen', 'region', '22-16272587') assert len(res['variants']) == 4 - # bad requests with pytest.raises(error.NotFoundError): utils.get_variant_list('SweGen', 'transcript', 'ENSTWEIRD') @@ -276,7 +275,8 @@ def test_remove_extraneous_vep_annotations(): """ annotation = [{'Consequence': 'frameshift_variant'}, {'Consequence': 'feature_elongation&TF_binding_site_variant'}] - assert utils.remove_extraneous_vep_annotations(annotation) == [{'Consequence': 'frameshift_variant'}] + assert utils.remove_extraneous_vep_annotations(annotation) == \ + [{'Consequence': 'frameshift_variant'}] def test_worst_csq_from_csq(): diff --git a/backend/modules/browser/utils.py b/backend/modules/browser/utils.py index d3c15aaf8..67055efd5 100644 --- a/backend/modules/browser/utils.py +++ b/backend/modules/browser/utils.py @@ -11,65 +11,63 @@ CHROMOSOMES = ['chr%s' % x for x in range(1, 23)] CHROMOSOMES.extend(['chrX', 'chrY', 'chrM']) -CHROMOSOME_TO_CODE = { item: i+1 for i, item in enumerate(CHROMOSOMES) } +CHROMOSOME_TO_CODE = {item: i+1 for i, item in enumerate(CHROMOSOMES)} # Note that this is the current as of v81 with some included for backwards compatibility (VEP <= 75) CSQ_ORDER = ["transcript_ablation", -"splice_acceptor_variant", -"splice_donor_variant", -"stop_gained", -"frameshift_variant", -"stop_lost", -"start_lost", # new in v81 -"initiator_codon_variant", # deprecated -"transcript_amplification", -"inframe_insertion", -"inframe_deletion", -"missense_variant", -"protein_altering_variant", # new in v79 -"splice_region_variant", -"incomplete_terminal_codon_variant", -"stop_retained_variant", -"synonymous_variant", -"coding_sequence_variant", -"mature_miRNA_variant", -"5_prime_UTR_variant", -"3_prime_UTR_variant", -"non_coding_transcript_exon_variant", -"non_coding_exon_variant", # deprecated -"intron_variant", -"NMD_transcript_variant", -"non_coding_transcript_variant", -"nc_transcript_variant", # deprecated -"upstream_gene_variant", -"downstream_gene_variant", -"TFBS_ablation", -"TFBS_amplification", -"TF_binding_site_variant", -"regulatory_region_ablation", -"regulatory_region_amplification", -"feature_elongation", -"regulatory_region_variant", -"feature_truncation", -"intergenic_variant", -""] - -CSQ_ORDER_DICT = {csq:i for i,csq in enumerate(CSQ_ORDER)} + "splice_acceptor_variant", + "splice_donor_variant", + "stop_gained", + "frameshift_variant", + "stop_lost", + "start_lost", # new in v81 + "initiator_codon_variant", # deprecated + "transcript_amplification", + "inframe_insertion", + "inframe_deletion", + "missense_variant", + "protein_altering_variant", # new in v79 + "splice_region_variant", + "incomplete_terminal_codon_variant", + "stop_retained_variant", + "synonymous_variant", + "coding_sequence_variant", + "mature_miRNA_variant", + "5_prime_UTR_variant", + "3_prime_UTR_variant", + "non_coding_transcript_exon_variant", + "non_coding_exon_variant", # deprecated + "intron_variant", + "NMD_transcript_variant", + "non_coding_transcript_variant", + "nc_transcript_variant", # deprecated + "upstream_gene_variant", + "downstream_gene_variant", + "TFBS_ablation", + "TFBS_amplification", + "TF_binding_site_variant", + "regulatory_region_ablation", + "regulatory_region_amplification", + "feature_elongation", + "regulatory_region_variant", + "feature_truncation", + "intergenic_variant", + ""] + +CSQ_ORDER_DICT = {csq: i for i, csq in enumerate(CSQ_ORDER)} REV_CSQ_ORDER_DICT = dict(enumerate(CSQ_ORDER)) -METRICS = [ - 'BaseQRankSum', - 'ClippingRankSum', - 'DP', - 'FS', - 'InbreedingCoeff', - 'MQ', - 'MQRankSum', - 'QD', - 'ReadPosRankSum', - 'VQSLOD' -] +METRICS = ['BaseQRankSum', + 'ClippingRankSum', + 'DP', + 'FS', + 'InbreedingCoeff', + 'MQ', + 'MQRankSum', + 'QD', + 'ReadPosRankSum', + 'VQSLOD'] PROTEIN_LETTERS_1TO3 = { 'A': 'Ala', 'C': 'Cys', 'D': 'Asp', 'E': 'Glu', @@ -81,9 +79,10 @@ } -def add_consequence_to_variants(variant_list:list): +def add_consequence_to_variants(variant_list: list): """ Add information about variant consequence to multiple variants. + Changes are performed in-place. Args: variant_list (list): list of variants @@ -94,9 +93,10 @@ def add_consequence_to_variants(variant_list:list): add_consequence_to_variant(variant) -def add_consequence_to_variant(variant:dict): +def add_consequence_to_variant(variant: dict): """ Add information about variant consequence to a variant. + Changes are performed in-place. Args: variant (dict): variant information @@ -108,7 +108,7 @@ def add_consequence_to_variant(variant:dict): variant['category'] = '' variant['flags'] = '' - if worst_csq is None: + if not worst_csq: return variant['major_consequence'] = worst_csq['major_consequence'] @@ -134,7 +134,7 @@ def add_consequence_to_variant(variant:dict): return -def annotation_severity(annotation:dict): +def annotation_severity(annotation: dict) -> float: """ Evaluate severity of the consequences; "bigger is more important". @@ -145,13 +145,13 @@ def annotation_severity(annotation:dict): float: severity score """ - rv = -CSQ_ORDER_DICT[worst_csq_from_csq(annotation['Consequence'])] + score = float(-CSQ_ORDER_DICT[worst_csq_from_csq(annotation['Consequence'])]) if annotation['CANONICAL'] == 'YES': - rv += 0.1 - return rv + score += 0.1 + return score -def get_coverage(dataset:str, datatype:str, item:str, ds_version:str=None): +def get_coverage(dataset: str, datatype: str, item: str, ds_version: str = None) -> dict: """ Retrieve coverage for a gene/region/transcript. @@ -165,7 +165,7 @@ def get_coverage(dataset:str, datatype:str, item:str, ds_version:str=None): dict: start, stop, coverage list """ - ret = {'coverage':[]} + ret: dict = {'coverage': []} if datatype == 'gene': gene = lookups.get_gene(dataset, item) @@ -173,12 +173,13 @@ def get_coverage(dataset:str, datatype:str, item:str, ds_version:str=None): transcript = lookups.get_transcript(dataset, gene['canonical_transcript']) if transcript: start = transcript['start'] - EXON_PADDING - stop = transcript['stop'] + EXON_PADDING - ret['coverage'] = lookups.get_coverage_for_transcript(dataset, transcript['chrom'], start, stop, ds_version) + stop = transcript['stop'] + EXON_PADDING + ret['coverage'] = lookups.get_coverage_for_transcript(dataset, transcript['chrom'], + start, stop, ds_version) elif datatype == 'region': chrom, start, stop = parse_region(item) - + if is_region_too_large(start, stop): raise error.MalformedRequest('Region too large') ret['coverage'] = lookups.get_coverage_for_bases(dataset, chrom, start, stop, ds_version) @@ -187,13 +188,14 @@ def get_coverage(dataset:str, datatype:str, item:str, ds_version:str=None): transcript = lookups.get_transcript(dataset, item) if transcript: start = transcript['start'] - EXON_PADDING - stop = transcript['stop'] + EXON_PADDING - ret['coverage'] = lookups.get_coverage_for_transcript(dataset, transcript['chrom'], start, stop, ds_version) + stop = transcript['stop'] + EXON_PADDING + ret['coverage'] = lookups.get_coverage_for_transcript(dataset, transcript['chrom'], + start, stop, ds_version) return ret -def get_coverage_pos(dataset:str, datatype:str, item:str, ds_version:str=None): +def get_coverage_pos(dataset: str, datatype: str, item: str, ds_version: str = None) -> dict: """ Retrieve coverage range. @@ -206,7 +208,7 @@ def get_coverage_pos(dataset:str, datatype:str, item:str, ds_version:str=None): dict: start, stop, chrom """ - ret = {'start':None, 'stop':None, 'chrom':None} + ret = {'start': None, 'stop': None, 'chrom': None} if datatype == 'region': chrom, start, stop = parse_region(item) @@ -223,13 +225,13 @@ def get_coverage_pos(dataset:str, datatype:str, item:str, ds_version:str=None): transcript = lookups.get_transcript(dataset, item, ds_version) if transcript: ret['start'] = transcript['start'] - EXON_PADDING - ret['stop'] = transcript['stop'] + EXON_PADDING + ret['stop'] = transcript['stop'] + EXON_PADDING ret['chrom'] = transcript['chrom'] return ret -def get_flags_from_variant(variant:dict): +def get_flags_from_variant(variant: dict) -> list: """ Get flags from variant. @@ -259,7 +261,7 @@ def get_flags_from_variant(variant:dict): return flags -def get_proper_hgvs(annotation:dict): +def get_proper_hgvs(annotation: dict) -> str: """ Get HGVS for change, either at transcript or protein level. @@ -278,10 +280,10 @@ def get_proper_hgvs(annotation:dict): return get_transcript_hgvs(annotation) return get_protein_hgvs(annotation) except KeyError: - return None + return '' -def get_protein_hgvs(annotation): +def get_protein_hgvs(annotation: dict) -> str: """ Aa changes in HGVS format. @@ -293,16 +295,16 @@ def get_protein_hgvs(annotation): """ try: - if '%3D' in annotation['HGVSp']: # "%3D" is "=" + if '%3D' in annotation['HGVSp']: # "%3D" is "=" amino_acids = ''.join([PROTEIN_LETTERS_1TO3[aa] for aa in annotation['Amino_acids']]) return "p." + amino_acids + annotation['Protein_position'] + amino_acids return annotation['HGVSp'].split(':')[-1] except KeyError: logging.error("Could not fetch protein hgvs") - return None + return '' -def get_transcript_hgvs(annotation:dict): +def get_transcript_hgvs(annotation: dict) -> str: """ Nucleotide change in HGVS format. @@ -316,10 +318,10 @@ def get_transcript_hgvs(annotation:dict): try: return annotation['HGVSc'].split(':')[-1] except KeyError: - return None + return '' -def get_variant_list(dataset:str, datatype:str, item:str, ds_version:str=None): +def get_variant_list(dataset: str, datatype: str, item: str, ds_version: str = None) -> dict: """ Retrieve variants for a datatype. @@ -333,10 +335,17 @@ def get_variant_list(dataset:str, datatype:str, item:str, ds_version:str=None): dict: {variants:list, headers:list} """ - headers = [['variant_id','Variant'], ['chrom','Chrom'], ['pos','Position'], - ['HGVS','Consequence'], ['filter','Filter'], ['major_consequence','Annotation'], - ['flags','Flags'], ['allele_count','Allele Count'], ['allele_num','Allele Number'], - ['hom_count','Number of Homozygous Alleles'], ['allele_freq','Allele Frequency']] + headers = [['variant_id', 'Variant'], + ['chrom', 'Chrom'], + ['pos', 'Position'], + ['HGVS', 'Consequence'], + ['filter', 'Filter'], + ['major_consequence', 'Annotation'], + ['flags', 'Flags'], + ['allele_count', 'Allele Count'], + ['allele_num', 'Allele Number'], + ['hom_count', 'Number of Homozygous Alleles'], + ['allele_freq', 'Allele Frequency']] if datatype == 'gene': variants = lookups.get_variants_in_gene(dataset, item, ds_version) @@ -350,11 +359,7 @@ def get_variant_list(dataset:str, datatype:str, item:str, ds_version:str=None): elif datatype == 'transcript': variants = lookups.get_variants_in_transcript(dataset, item, ds_version) - - if datatype == 'transcript': transcript = lookups.get_transcript(dataset, item, ds_version) - if not transcript: - return None refgene = transcript['gene_id'] if variants: @@ -377,19 +382,19 @@ def get_variant_list(dataset:str, datatype:str, item:str, ds_version:str=None): # Format output def format_variant(variant): - variant['major_consequence'] = (variant['major_consequence'].replace('_variant','') + variant['major_consequence'] = (variant['major_consequence'].replace('_variant', '') .replace('_prime_', '\'') .replace('_', ' ')) # This is so an array values turns into a comma separated string instead - return {k: ", ".join(v) if isinstance(v,list) else v for k, v in variant.items()} + return {k: ", ".join(v) if isinstance(v, list) else v for k, v in variant.items()} variants = list(map(format_variant, variants)) return {'variants': variants, 'headers': headers} -def order_vep_by_csq(annotation_list:list): +def order_vep_by_csq(annotation_list: list) -> list: """ Will add "major_consequence" to each annotation and order by severity. @@ -405,10 +410,10 @@ def order_vep_by_csq(annotation_list:list): ann['major_consequence'] = worst_csq_from_csq(ann['Consequence']) except KeyError: ann['major_consequence'] = '' - return sorted(annotation_list, key=(lambda ann:CSQ_ORDER_DICT[ann['major_consequence']])) + return sorted(annotation_list, key=(lambda ann: CSQ_ORDER_DICT[ann['major_consequence']])) -def is_region_too_large(start:int, stop:int): +def is_region_too_large(start: int, stop: int) -> bool: """ Evaluate whether the size of a region is larger than maximum query. @@ -424,7 +429,7 @@ def is_region_too_large(start:int, stop:int): return int(stop)-int(start) > region_limit -def parse_dataset(dataset:str, ds_version:str=None): +def parse_dataset(dataset: str, ds_version: str = None) -> tuple: """ Check/parse if the dataset name is in the beacon form (``reference:dataset:version``). @@ -442,7 +447,7 @@ def parse_dataset(dataset:str, ds_version:str=None): return (dataset, ds_version) -def parse_region(region:str): +def parse_region(region: str) -> tuple: """ Parse a region with either one or two positions @@ -453,26 +458,28 @@ def parse_region(region:str): tuple: (chrom, start, pos) """ parts = region.split('-') + if len(parts) == 2: - chrom, start = parts - stop = start + chrom, str_start = parts + str_stop = str_start elif len(parts) == 3: - chrom, start, stop = parts + chrom, str_start, str_stop = parts else: raise error.ParsingError(f'Unable to parse region {region}.') try: - start = int(start) - stop = int(stop) - except ValueError: - raise error.ParsingError(f'Unable to parse region {region} (positions not integers).') - + start = int(str_start) + stop = int(str_stop) + except ValueError as err: + raise error.ParsingError(f'Unable to parse region {region} (pos not integers).') from err + return chrom, start, stop -def remove_extraneous_information(variant:dict): +def remove_extraneous_information(variant: dict): """ Remove information that is not used in the frontend from a variant. + Changes are performed in-place. Args: variant (dict): variant data from database @@ -485,7 +492,7 @@ def remove_extraneous_information(variant:dict): del variant['vep_annotations'] -def remove_extraneous_vep_annotations(annotation_list:list): +def remove_extraneous_vep_annotations(annotation_list: list) -> list: """ Remove annotations with low-impact consequences (less than intron variant). @@ -500,7 +507,7 @@ def remove_extraneous_vep_annotations(annotation_list:list): if worst_csq_index(ann['Consequence'].split('&')) <= CSQ_ORDER_DICT['intron_variant']] -def worst_csq_from_list(csq_list:list): +def worst_csq_from_list(csq_list: list) -> str: """ Choose the worst consequence. @@ -514,7 +521,7 @@ def worst_csq_from_list(csq_list:list): return REV_CSQ_ORDER_DICT[worst_csq_index(csq_list)] -def worst_csq_from_csq(csq:str): +def worst_csq_from_csq(csq: str) -> str: """ Find worst consequence in a possibly &-filled consequence string. @@ -528,7 +535,7 @@ def worst_csq_from_csq(csq:str): return REV_CSQ_ORDER_DICT[worst_csq_index(csq.split('&'))] -def worst_csq_index(csq_list:list): +def worst_csq_index(csq_list: list) -> int: """ Find the index of the worst consequence. @@ -544,7 +551,7 @@ def worst_csq_index(csq_list:list): return min([CSQ_ORDER_DICT[csq] for csq in csq_list]) -def worst_csq_with_vep(annotation_list:list): +def worst_csq_with_vep(annotation_list: list) -> dict: """ Choose the vep annotation with the most severe consequence. @@ -558,7 +565,7 @@ def worst_csq_with_vep(annotation_list:list): """ if not annotation_list: - return None + return {} worst = max(annotation_list, key=annotation_severity) worst['major_consequence'] = worst_csq_from_csq(worst['Consequence']) return worst diff --git a/backend/route.py b/backend/route.py index bf75d164f..f21e3e31d 100644 --- a/backend/route.py +++ b/backend/route.py @@ -1,10 +1,11 @@ import logging +import sys + import tornado.httpserver import tornado.ioloop -import tornado.web from tornado.options import define, options +import tornado.web -import sys import application import handlers import auth @@ -16,78 +17,80 @@ define("develop", default=False, help="Run in develop environment", type=bool) # Setup the Tornado Application +# pylint: disable=no-member tornado_settings = {"debug": False, - "cookie_secret": swefreq_settings.cookie_secret, - "login_url": "/login", - "elixir_oauth": { - "id": swefreq_settings.elixir["id"], - "secret": swefreq_settings.elixir["secret"], - "redirect_uri": swefreq_settings.elixir["redirectUri"], - }, - "xsrf_cookies": True, - "template_path": "templates/", - } + "cookie_secret": swefreq_settings.cookie_secret, + "login_url": "/login", + "elixir_oauth": { + "id": swefreq_settings.elixir["id"], + "secret": swefreq_settings.elixir["secret"], + "redirect_uri": swefreq_settings.elixir["redirectUri"], + }, + "xsrf_cookies": True, + "template_path": "templates/"} +# pylint: enable=no-member + +# pylint: disable=line-too-long class Application(tornado.web.Application): def __init__(self, settings): self.declared_handlers = [ - ## Static handlers - (r"/static/(.*)", tornado.web.StaticFileHandler, - {"path": "static/"}), - (r'/(favicon.ico)', tornado.web.StaticFileHandler, - {"path": "static/img/"}), - (r"/release/(?P[^\/]+)/versions/(?P[^/]+)/(?P[^\/]+)/(?P[^\/]+)", handlers.TemporaryStaticNginxFileHandler, - {"path": "/release-files/"}), - (r"/release/(?P[^\/]+)/versions/(?P[^/]+)/(?P[^\/]+)", handlers.AuthorizedStaticNginxFileHandler, - {"path": "/release-files/"}), - ## Authentication - (r"/logout", auth.ElixirLogoutHandler), - (r"/elixir/login", auth.ElixirLoginHandler), - (r"/elixir/logout", auth.ElixirLogoutHandler), - ## API Methods - (r"/api/countries", application.CountryList), - (r"/api/users/me", application.GetUser), - (r"/api/users/datasets", application.UserDatasetAccess), - (r"/api/users/sftp_access", application.SFTPAccess), - (r"/api/schema", application.GetSchema), - ### Dataset Api - (r"/api/dataset", application.ListDatasets), - (r"/api/dataset/(?P[^\/]+)", application.GetDataset), + # Static handlers + (r"/static/(.*)", tornado.web.StaticFileHandler, {"path": "static/"}), + (r'/(favicon.ico)', tornado.web.StaticFileHandler, {"path": "static/img/"}), + (r"/release/(?P[^\/]+)/versions/(?P[^/]+)/(?P[^\/]+)/(?P[^\/]+)", + handlers.TemporaryStaticNginxFileHandler, + {"path": "/release-files/"}), + (r"/release/(?P[^\/]+)/versions/(?P[^/]+)/(?P[^\/]+)", + handlers.AuthorizedStaticNginxFileHandler, + {"path": "/release-files/"}), + # Authentication + (r"/logout", auth.ElixirLogoutHandler), + (r"/elixir/login", auth.ElixirLoginHandler), + (r"/elixir/logout", auth.ElixirLogoutHandler), + # API Methods + (r"/api/countries", application.CountryList), + (r"/api/users/me", application.GetUser), + (r"/api/users/datasets", application.UserDatasetAccess), + (r"/api/users/sftp_access", application.SFTPAccess), + (r"/api/schema", application.GetSchema), + # Dataset Api + (r"/api/dataset", application.ListDatasets), + (r"/api/dataset/(?P[^\/]+)", application.GetDataset), (r"/api/dataset/(?P[^\/]+)/log/(?P[^\/]+)/(?P[^\/]+)", application.LogEvent), - (r"/api/dataset/(?P[^\/]+)/logo", application.ServeLogo), + (r"/api/dataset/(?P[^\/]+)/logo", application.ServeLogo), (r"/api/dataset/(?P[^\/]+)/(?:versions/(?P[^/]+)/)?files", application.DatasetFiles), (r"/api/dataset/(?P[^\/]+)/(?:versions/(?P[^/]+)/)?collection", application.Collection), - (r"/api/dataset/(?P[^\/]+)/users_current", application.DatasetUsersCurrent), - (r"/api/dataset/(?P[^\/]+)/users_pending", application.DatasetUsersPending), + (r"/api/dataset/(?P[^\/]+)/users_current", application.DatasetUsersCurrent), + (r"/api/dataset/(?P[^\/]+)/users_pending", application.DatasetUsersPending), (r"/api/dataset/(?P[^\/]+)/(?:versions/(?P[^/]+)/)?temporary_link", application.GenerateTemporaryLink), - (r"/api/dataset/(?P[^\/]+)/users/[^\/]+/request", application.RequestAccess), - (r"/api/dataset/(?P[^\/]+)/users/(?P[^\/]+)/approve", application.ApproveUser), - (r"/api/dataset/(?P[^\/]+)/users/(?P[^\/]+)/revoke", application.RevokeUser), - (r"/api/dataset/(?P[^\/]+)/versions", application.ListDatasetVersions), - (r"/api/dataset/(?P[^\/]+)/versions/(?P[^\/]+)", application.GetDataset), + (r"/api/dataset/(?P[^\/]+)/users/[^\/]+/request", application.RequestAccess), + (r"/api/dataset/(?P[^\/]+)/users/(?P[^\/]+)/approve", application.ApproveUser), + (r"/api/dataset/(?P[^\/]+)/users/(?P[^\/]+)/revoke", application.RevokeUser), + (r"/api/dataset/(?P[^\/]+)/versions", application.ListDatasetVersions), + (r"/api/dataset/(?P[^\/]+)/versions/(?P[^\/]+)", application.GetDataset), (r"/api/dataset/(?P[^\/]+)/versions/(?P[^\/]+)/files", application.DatasetFiles), (r"/api/dataset/(?P[^\/]+)/versions/(?P[^\/]+)/temporary_link", application.GenerateTemporaryLink), ] - ## Adding module handlers + # Adding module handlers self.declared_handlers += browser_routes - ## Adding Catch all handlers + # Adding Catch all handlers self.declared_handlers += [ - (r"/api/.*", tornado.web.ErrorHandler, - {"status_code": 404} ), - (r'().*', tornado.web.StaticFileHandler, - {"path": "static/templates/", "default_filename": "index.html"}), + (r"/api/.*", tornado.web.ErrorHandler, {"status_code": 404}), + (r'().*', tornado.web.StaticFileHandler, {"path": "static/templates/", "default_filename": "index.html"}), ] - ## Adding developer login handler + # Adding developer login handler if settings.get('develop', False): self.declared_handlers.insert(-1, ("/developer/login", auth.DeveloperLoginHandler)) - self.declared_handlers.insert(-1, ("/developer/quit", application.QuitHandler)) + self.declared_handlers.insert(-1, ("/developer/quit", application.QuitHandler)) # Setup the Tornado Application tornado.web.Application.__init__(self, self.declared_handlers, **settings) + if __name__ == '__main__': # Make sure that the extra option to `settings` isn't upsetting tornado if '--settings_file' in sys.argv: @@ -105,8 +108,8 @@ def __init__(self, settings): logging.getLogger().setLevel(logging.DEBUG) # Instantiate Application - application = Application(tornado_settings) - application.listen(options.port, xheaders=True) + tornado_application = Application(tornado_settings) + tornado_application.listen(options.port, xheaders=True) # Get a handle to the instance of IOLoop ioloop = tornado.ioloop.IOLoop.instance() diff --git a/backend/settings.py b/backend/settings.py index c6543e4b5..d9482b8b2 100644 --- a/backend/settings.py +++ b/backend/settings.py @@ -24,7 +24,7 @@ elixir = json_settings["elixir"] -## Generated with base64.b64encode(uuid.uuid4().bytes + uuid.uuid4().bytes) +# Generated with base64.b64encode(uuid.uuid4().bytes + uuid.uuid4().bytes) cookie_secret = json_settings["cookieSecret"] # PostgreSQL settings @@ -34,13 +34,6 @@ psql_user = json_settings["postgresUser"] psql_pass = json_settings["postgresPass"] -# MySql settings -mysql_host = json_settings["mysqlHost"] -mysql_schema = json_settings["mysqlSchema"] -mysql_user = json_settings["mysqlUser"] -mysql_passwd = json_settings["mysqlPasswd"] -mysql_port = json_settings["mysqlPort"] - # e-mail config mail_server = json_settings["mailServer"] from_address = json_settings["fromAddress"] diff --git a/backend/test.py b/backend/test.py index 243ebd318..64b0b41f8 100644 --- a/backend/test.py +++ b/backend/test.py @@ -43,8 +43,8 @@ def assertHTTPCode(self, path, code=200, method='get', *args, **kwargs): r = m(path, *args, **kwargs) self.assertEqual(r.status_code, code) - def login_user(self,user): - self.assertHTTPCode('/developer/login?user={}&email={}'.format(user,user), 200) + def login_user(self, user): + self.assertHTTPCode(f'/developer/login?user={user}&email={user}', 200) class TestEndpoints(RequestTests): @@ -89,7 +89,7 @@ def test_user_datasets(self): class TestRequestAccess(RequestTests): - USER='e1' + USER = 'e1' def setUp(self): self.newSession() @@ -99,7 +99,7 @@ def setUp(self): def tearDown(self): self.destroySession() try: - u = db.User.select(db.User).where(db.User.email==self.USER).get() + u = db.User.select(db.User).where(db.User.email == self.USER).get() try: u.dataset_access.get().delete_instance() except peewee.PeeweeException: @@ -119,11 +119,10 @@ def tearDown(self): if not db.database.is_closed(): db.database.close() - def test_login(self): self.login_user(self.USER) - count = db.User.select().where(db.User.email==self.USER).count() + count = db.User.select().where(db.User.email == self.USER).count() self.assertEqual(count, 0) self.assertIn('email', self.cookies) @@ -136,12 +135,9 @@ def test_request_access_with_get(self): def test_request_access_without_xsrf(self): self.login_user(self.USER) r = self.post('/api/dataset/Dataset 1/users/{}/request'.format(self.USER), - data = { - "affiliation": 'none', - "country": "Sweden", - "newsletter": 0, - } - ) + data={"affiliation": 'none', + "country": "Sweden", + "newsletter": 0}) self.assertEqual(r.status_code, 403) def test_get_xsrf_token(self): @@ -151,13 +147,10 @@ def test_get_xsrf_token(self): def test_request_access_with_wrong_xsrf_1(self): self.login_user(self.USER) r = self.post('/api/dataset/Dataset 1/users/{}/request'.format(self.USER), - data = { - "affiliation": 'none', - "country": "Sweden", - "newsletter": 0, - "_xsrf": 'Fnurken', - } - ) + data={"affiliation": 'none', + "country": "Sweden", + "newsletter": 0, + "_xsrf": 'Fnurken'}) self.assertEqual(r.status_code, 403) def test_request_access_with_wrong_xsrf_2(self): @@ -168,32 +161,26 @@ def test_request_access_with_wrong_xsrf_2(self): self.assertIn('email', self.cookies) r = self.post('/api/dataset/Dataset 1/users/{}/request'.format(self.USER), - data = { - "affiliation": 'none', - "country": "Sweden", - "newsletter": 0, - "_xsrf": 'Fnurken', - } - ) + data={"affiliation": 'none', + "country": "Sweden", + "newsletter": 0, + "_xsrf": 'Fnurken'}) self.assertEqual(r.status_code, 403) def test_request_access_correctly(self): self.login_user(self.USER) - count = db.User.select().where(db.User.email==self.USER).count() + count = db.User.select().where(db.User.email == self.USER).count() self.assertEqual(count, 0) r = self.post('/api/dataset/Dataset 1/users/{}/request'.format(self.USER), - data = { - "affiliation": 'none', - "country": "Sweden", - "newsletter": 0, - "_xsrf": self.cookies['_xsrf'], - } - ) + data={"affiliation": 'none', + "country": "Sweden", + "newsletter": 0, + "_xsrf": self.cookies['_xsrf']}) self.assertEqual(r.status_code, 200) - count = db.User.select().where(db.User.email==self.USER).count() + count = db.User.select().where(db.User.email == self.USER).count() self.assertEqual(count, 1) r = self.get('/api/users/datasets') @@ -289,12 +276,10 @@ def tearDown(self): if hasattr(self, '_email'): al = (db.UserAccessLog.select() - .join(db.User) - .where( - ( (db.UserAccessLog.action == 'access_granted') + .join(db.User) + .where(((db.UserAccessLog.action == 'access_granted') | (db.UserAccessLog.action == 'access_revoked')) - & (db.User.email == self._email) - )) + & (db.User.email == self._email))) for a in al: a.delete_instance() @@ -308,16 +293,15 @@ def test_admin_approve_user(self): self.assertHTTPCode('/api/dataset/Dataset%201/users/{}/approve'.format(email), 405) self.assertHTTPCode('/api/dataset/Dataset%201/users/{}/approve'.format(email), 403, 'POST') self.assertHTTPCode('/api/dataset/Dataset%201/users/{}/approve'.format(email), 403, 'POST', - data = {'_xsrf': "The wrong thing"} ) + data={'_xsrf': "The wrong thing"}) self.assertHTTPCode('/api/dataset/Dataset%201/users/{}/approve'.format(email), 200, 'POST', - data = {'_xsrf': self.cookies['_xsrf']} ) - + data={'_xsrf': self.cookies['_xsrf']}) r = self.get('/api/dataset/Dataset%201/users_current') - l = [u for u in r.json()['data'] if u['email'] == email] + data_list = [val for val in r.json()['data'] if val['email'] == email] - self.assertEqual(len(l), 1) + self.assertEqual(len(data_list), 1) def test_recently_approved_user_can_list_files(self): self.login_user('admin1') @@ -331,8 +315,8 @@ def test_recently_approved_user_can_list_files(self): self.newSession() self.login_user('admin1') - self.assertHTTPCode('/api/dataset/Dataset%201/users/{}/approve'.format(u['email']), 200, 'POST', - data = {'_xsrf': self.cookies['_xsrf']} ) + self.assertHTTPCode(f'/api/dataset/Dataset%201/users/{u["email"]}/approve', 200, 'POST', + data={'_xsrf': self.cookies['_xsrf']}) self.newSession() self.login_user(u['email']) @@ -361,8 +345,8 @@ def test_recently_revoked_user_cant_list_files(self): self.newSession() self.login_user('admin1') - self.assertHTTPCode('/api/dataset/Dataset%201/users/{}/revoke'.format(u['email']), 200, 'POST', - data = {'_xsrf': self.cookies['_xsrf']} ) + self.assertHTTPCode(f'/api/dataset/Dataset%201/users/{u["email"]}/revoke', 200, 'POST', + data={'_xsrf': self.cookies['_xsrf']}) self.newSession() self.login_user(u['email']) @@ -372,35 +356,32 @@ def test_full_user_roundabout(self): email = 'unlisted' self._email = email - ## Request access + # Request access self.assertHTTPCode('/api/dataset/Dataset%201/files', 403) self.login_user(email) self.assertHTTPCode('/api/dataset/Dataset%201/files', 403) - self.assertHTTPCode('/api/dataset/Dataset 1/users/{}/request'.format(email), 200, 'POST', - data = { - "affiliation": 'none', - "country": "Sweden", - "newsletter": 0, - "_xsrf": self.cookies['_xsrf'], - } - ) + self.assertHTTPCode(f'/api/dataset/Dataset 1/users/{email}/request', 200, 'POST', + data={"affiliation": 'none', + "country": "Sweden", + "newsletter": 0, + "_xsrf": self.cookies['_xsrf']}) self.assertHTTPCode('/api/dataset/Dataset%201/files', 403) - ## Approve user + # Approve user self.newSession() self.login_user('admin1') # User is in pending queue users = self.get('/api/dataset/Dataset%201/users_pending').json()['data'] - u = [ x for x in users if x['email'] == email ] + u = [x for x in users if x['email'] == email] self.assertEqual(len(u), 1) - self.assertHTTPCode('/api/dataset/Dataset%201/users/{}/approve'.format(email), 200, 'POST', - data = {'_xsrf': self.cookies['_xsrf']} ) + self.assertHTTPCode(f'/api/dataset/Dataset%201/users/{email}/approve', 200, 'POST', + data={'_xsrf': self.cookies['_xsrf']}) # User is in approved queue users = self.get('/api/dataset/Dataset%201/users_current').json()['data'] - u = [ x for x in users if x['email'] == email ] + u = [x for x in users if x['email'] == email] self.assertEqual(len(u), 1) # User can log in and do stuff @@ -412,11 +393,11 @@ def test_full_user_roundabout(self): self.newSession() self.login_user('admin1') self.assertHTTPCode('/api/dataset/Dataset%201/users/{}/revoke'.format(email), 200, 'POST', - data = {'_xsrf': self.cookies['_xsrf']} ) + data={'_xsrf': self.cookies['_xsrf']}) # User is not in approved queue users = self.get('/api/dataset/Dataset%201/users_current').json()['data'] - u = [ x for x in users if x['email'] == email ] + u = [x for x in users if x['email'] == email] self.assertEqual(len(u), 0) # User can log in but cant do stuff @@ -450,11 +431,11 @@ def testLoggedInTempLinkPost(self): def testLoggedInTempLinkPostXSRF1(self): self.assertHTTPCode('/api/dataset/Dataset 1/temporary_link', 403, 'POST', - data = { '_xsrf': "INCORRECT"}) + data={'_xsrf': "INCORRECT"}) def testLoggedInTempLinkPostXSRF2(self): self.assertHTTPCode('/api/dataset/Dataset 1/temporary_link', 200, 'POST', - data = {'_xsrf': self.cookies['_xsrf']} ) + data={'_xsrf': self.cookies['_xsrf']}) if __name__ == '__main__': diff --git a/backend/tests/test_application.py b/backend/tests/test_application.py new file mode 100644 index 000000000..b00df0a4a --- /dev/null +++ b/backend/tests/test_application.py @@ -0,0 +1,138 @@ +""" +Test the browser handlers +""" +import json + +import requests + +BASE_URL = "http://localhost:4000" + +def test_get_schema(): + """ + Test GetSchema.get() + """ + response = requests.get(f'{BASE_URL}/api/schema') + data = json.loads(response.text) + expected = {'@context': 'http://schema.org/', + '@type': 'DataCatalog', + 'name': 'SweFreq', + 'alternateName': ['The Swedish Frequency resource for genomics']} + assert len(data) == 10 + for value in expected: + assert data[value] == expected[value] + + ds_name = 'SweGen' + response = requests.get(f'{BASE_URL}/api/schema?url={BASE_URL}/dataset/{ds_name}/browser') + data = json.loads(response.text) + expected = {"@type": "Dataset", + "url": f"{BASE_URL}/dataset/{ds_name}", + "@id": f"{BASE_URL}/dataset/{ds_name}", + "name": f"{ds_name}", + "description": "desc", + "identifier": f"{ds_name}", + "citation": "doi"} + assert data['dataset'] == expected + + response = requests.get(f'{BASE_URL}/api/schema?url={BASE_URL}/dataset/{ds_name}/version/123456/browser') + assert not response.text + assert response.status_code == 404 + + response = requests.get(f'{BASE_URL}/api/schema?url={BASE_URL}/dataset/bad_ds_name/browser') + assert not response.text + assert response.status_code == 404 + + ds_name = 'SweGen2' + response = requests.get(f'{BASE_URL}/api/schema?url={BASE_URL}/dataset/{ds_name}/version/UNRELEASED/browser') + assert not response.text + assert response.status_code == 403 + + response = requests.get(f'{BASE_URL}/api/schema?url={BASE_URL}/dataset/{ds_name}/beacon') + data = json.loads(response.text) + expected = {'@id': 'https://swefreq.nbis.se/api/beacon-elixir/', + '@type': 'Beacon', + 'dct:conformsTo': 'https://bioschemas.org/specifications/drafts/Beacon/', + 'name': 'Swefreq Beacon', + 'provider': {'@type': 'Organization', + 'name': 'National Bioinformatics Infrastructure Sweden', + 'alternateName': ['NBIS', 'ELIXIR Sweden'], + 'logo': 'http://nbis.se/assets/img/logos/nbislogo-green.svg', + 'url': 'https://nbis.se/'}, + 'supportedRefs': ['GRCh37'], + 'description': 'Beacon API Web Server based on the GA4GH Beacon API', + 'aggregator': False, + 'url': 'https://swefreq.nbis.se/api/beacon-elixir/'} + for value in expected: + assert data[value] == expected[value] + + +def test_get_countrylist(): + """ + Test CountryList.get() + """ + response = requests.get(f'{BASE_URL}/api/countries') + data = json.loads(response.text) + + assert len(data['countries']) == 240 + + +def test_get_dataset(): + """ + Test GetDataset.get() + """ + ds_name = 'SweGen' + response = requests.get(f'{BASE_URL}/api/dataset/{ds_name}') + data = json.loads(response.text) + expected = {"study": 1, + "shortName": "SweGen", + "fullName": "SweGen", + "version": {"version": "20180409", + "description": "desc", + "terms": "terms", + "availableFrom": "2001-01-04", + "refDoi": "doi", + "dataContactName": "place", + "dataContactLink": "email", + "numVariants": None, + "coverageLevels": [1, 5, 10, 15, 20, 25, 30, 50, 100], + "portalAvail": True, + "fileAccess": "REGISTERED", + "beaconAccess": "PUBLIC", + "dataset": 1, + "referenceSet": 1, + "varCallRef": None}, + "future": False} + for value in expected: + assert data[value] == expected[value] + assert len(data) == 14 + + ds_name = 'SweGen2' + response = requests.get(f'{BASE_URL}/api/dataset/{ds_name}') + data = json.loads(response.text) + expected = {"study": 1, + "shortName": "SweGen2", + "fullName": "SweGen2", + "version": {"version": "20190409", + "description": "desc", + "terms": "terms", + "availableFrom": "2001-01-05", + "refDoi": "doi", + "dataContactName": "place", + "dataContactLink": "email", + "numVariants": None, + "coverageLevels": [1, 5, 10, 15, 20, 25, 30, 50, 100], + "portalAvail": True, + "fileAccess": "REGISTERED", + "beaconAccess": "PUBLIC", + "dataset": 2, + "referenceSet": 1, + "varCallRef":None}, + "future": False} + for value in expected: + assert data[value] == expected[value] + assert len(data) == 14 + + ds_name = 'Unrel' + response = requests.get(f'{BASE_URL}/api/dataset/{ds_name}') + assert not response.text + assert response.status_code == 404 + diff --git a/frontend/src/js/controller.browserController.js b/frontend/src/js/controller.browserController.js index 89b40003b..5de46a03e 100644 --- a/frontend/src/js/controller.browserController.js +++ b/frontend/src/js/controller.browserController.js @@ -55,95 +55,95 @@ localThis.itemType = "transcript"; localThis.item = $routeParams.transcript; Browser.getTranscript($routeParams.dataset, $routeParams.version, $routeParams.transcript) - .then( function(data) { + .then( function(data) { localThis.transcript = data.transcript; localThis.gene = data.gene; localThis.coverage.region.exons = data.exons; }) - .catch((err) => { + .catch((err) => { localThis.transcript = {"statusCode": err.status, "statusText": err.statusText}; - }); -; + }); + } if ($routeParams.region) { localThis.itemType = "region"; localThis.item = $routeParams.region; Browser.getRegion($routeParams.dataset, $routeParams.version, $routeParams.region) - .then( function(data) { + .then( function(data) { localThis.region = data.region; }) - .catch((err) => { + .catch((err) => { localThis.region = {"statusCode": err.status, - "statusText": err.statusText, - "variantId": $routeParams.region}; - }); + "statusText": err.statusText, + "variantId": $routeParams.region}; + }); } if ($routeParams.gene) { localThis.itemType = "gene"; localThis.item = $routeParams.gene; Browser.getGene($routeParams.dataset, $routeParams.version, $routeParams.gene) - .then( function(data) { + .then( function(data) { localThis.gene = data.gene; localThis.transcripts = data.transcripts; localThis.coverage.region.exons = data.exons; }) - .catch((err) => { + .catch((err) => { localThis.gene = {"statusCode": err.status, - "statusText": err.statusText}; - }); + "statusText": err.statusText}; + }); } if (localThis.itemType) { Browser.getVariants($routeParams.dataset, $routeParams.version, localThis.itemType, localThis.item) - .then( function(data) { + .then( function(data) { localThis.variants = data.variants; localThis.headers = data.headers; // TODO Move to function later let mapFunction = function(variant) { variant.isPass = variant.filter == "PASS"; - if (variant.flags.indexOf("LoF") === -1) - variant.isLof = false; - else - variant.isLof = true; + if (variant.flags.indexOf("LoF") === -1) + variant.isLof = false; + else + variant.isLof = true; variant.isMissense = variant.majorConsequence == "missense"; }; localThis.variants.map(mapFunction); localThis.filterVariants(); - localThis.variants.loaded = true; + localThis.variants.loaded = true; }) - .catch((err) => { - localThis.variants = {"statusCode": err.status, - "statusText": err.statusText, - "loaded": true,}; - }); + .catch((err) => { + localThis.variants = {"statusCode": err.status, + "statusText": err.statusText, + "loaded": true,}; + }); Browser.getCoveragePos($routeParams.dataset, $routeParams.version, localThis.itemType, localThis.item) - .then( function(data) { + .then( function(data) { localThis.coverage.region.start = data.start; localThis.coverage.region.stop = data.stop; localThis.coverage.region.chrom = data.chrom; }); Browser.getCoverage($routeParams.dataset, $routeParams.version, localThis.itemType, localThis.item) - .then(function(data) { + .then(function(data) { localThis.coverage.data = data.coverage; localThis.coverage.loaded = true; }) - .catch((err) => { - localThis.coverage = {"statusCode": err.status, - "statusText": err.statusText, - "loaded": true,}; - }); + .catch((err) => { + localThis.coverage = {"statusCode": err.status, + "statusText": err.statusText, + "loaded": true,}; + }); } if ($routeParams.variant) { Browser.getVariant($routeParams.dataset, $routeParams.version, $routeParams.variant) - .then( function(data) { + .then( function(data) { localThis.variant = data.variant; }) - .catch((err) => { - localThis.variant = {"statusCode": err.status, - "statusText": err.statusText}; - }); + .catch((err) => { + localThis.variant = {"statusCode": err.status, + "statusText": err.statusText}; + }); } Dataset.getDataset($routeParams.dataset, $routeParams.version, $routeParams.version) diff --git a/frontend/src/js/controller.datasetBeaconController.js b/frontend/src/js/controller.datasetBeaconController.js index d194c395f..a7b08635c 100644 --- a/frontend/src/js/controller.datasetBeaconController.js +++ b/frontend/src/js/controller.datasetBeaconController.js @@ -12,9 +12,9 @@ function activate() { Beacon.getBeaconReferences($routeParams.dataset, $routeParams.version) .then(function(data) { - if (data) { + if (data) { localThis.beaconInfo = data; - } + } }); User.getUser().then(function(data) { @@ -34,7 +34,7 @@ function search() { Beacon.queryBeacon(localThis) .then(function(response) { - if (response.data.exists===false) { // value may be null -> error + if (response.data.exists===false) { // value may be null -> error localThis.queryResponses.push({ "response": { "state": "Absent" }, "query": { @@ -44,19 +44,19 @@ "referenceAllele": localThis.referenceAllele, } }); - } - else if (response.data.exists===true) { + } + else if (response.data.exists===true) { localThis.queryResponses.push({ - "response": { "state": "Present" }, - "query": { + "response": { "state": "Present" }, + "query": { "chromosome": localThis.chromosome, "position": localThis.position, "allele": localThis.allele, "referenceAllele": localThis.referenceAllele, } }); - } - else { + } + else { localThis.queryResponses.push({ "response": { "state": "Error" }, "query": { @@ -82,10 +82,10 @@ ); } function fillExample() { - localThis.chromosome = "22"; - localThis.position = 46615880; - localThis.referenceAllele = "T"; - localThis.allele = "C"; + localThis.chromosome = "22"; + localThis.position = 46615880; + localThis.referenceAllele = "T"; + localThis.allele = "C"; } }]); })(); diff --git a/frontend/src/js/controller.datasetDownloadController.js b/frontend/src/js/controller.datasetDownloadController.js index 3336bcbdc..21f97f20a 100644 --- a/frontend/src/js/controller.datasetDownloadController.js +++ b/frontend/src/js/controller.datasetDownloadController.js @@ -44,10 +44,10 @@ } function updateAuthorizationLevel() { - if (!localThis.hasOwnProperty("user") || localThis.user.user == null) { + if (!Object.prototype.hasOwnProperty.call(localThis, "user") || localThis.user.user == null) { localThis.authorizationLevel = "logged_out"; } - else if (localThis.hasOwnProperty("dataset")) { + else if (Object.prototype.hasOwnProperty.call(localThis, "dataset")) { localThis.authorizationLevel = localThis.dataset.authorizationLevel; } } @@ -89,7 +89,7 @@ } function dataContactIsEmail() { - return localThis.hasOwnProperty("dataset") && + return Object.prototype.hasOwnProperty.call(localThis, "dataset") && localThis.dataset.version.dataContactLink.indexOf("@") > -1; } }]); diff --git a/frontend/src/js/factory.beacon.js b/frontend/src/js/factory.beacon.js index 066a1e91e..a97b3b650 100644 --- a/frontend/src/js/factory.beacon.js +++ b/frontend/src/js/factory.beacon.js @@ -8,41 +8,42 @@ function getBeaconReferences(name, version) { return $http.get("/api/beacon-elixir/").then(function(data) { - var d = data.data.datasets; + let d = data.data.datasets; if (version) { - for (var i = 0; i < d.length; i++) { - var dataset = d[i].id; + for (let i = 0; i < d.length; i++) { + let dataset = d[i].id; if (dataset.indexOf(name) != -1 && dataset.indexOf(version) != -1) { - return { - "reference": dataset.split(":")[0].substring(0, 6), - "datasetId": dataset, - } + return { + "reference": dataset.split(":")[0].substring(0, 6), + "datasetId": dataset, + }; } } } else { - var references = []; - for (var i = 0; i < d.length; i++) { - var dataset = d[i].id; + let references = []; + for (let i = 0; i < d.length; i++) { + let dataset = d[i].id; if (dataset.indexOf(name) !== -1) { - references.push(dataset); + references.push(dataset); } } - var highest_ver = 0; - var reference = ""; - for (var i = 0; i < references.length; i++) { - var ver = parseInt(references[i].split(":")[2]); - if (ver > highest_ver) { - highest_ver = ver; - reference = references[i].split(":")[0].substring(0, 6); - beaconId = references[i]; + let beaconId = ""; + let highestVer = 0; + let reference = ""; + for (let i = 0; i < references.length; i++) { + let ver = parseInt(references[i].split(":")[2]); + if (ver > highestVer) { + highestVer = ver; + reference = references[i].split(":")[0].substring(0, 6); + beaconId = references[i]; } - } - return { + } + return { "reference": reference, "datasetId": beaconId, - } + }; } }); } diff --git a/frontend/src/js/factory.browser.js b/frontend/src/js/factory.browser.js index c5f1fba79..99ef4246a 100644 --- a/frontend/src/js/factory.browser.js +++ b/frontend/src/js/factory.browser.js @@ -14,16 +14,16 @@ }; function baseUrl(dataset, version) { - var url = "/api/dataset/" + dataset + "/"; - if ( version ) { - url += "version/" + version + "/" - } - url += 'browser/'; - return url; + var url = "/api/dataset/" + dataset + "/"; + if ( version ) { + url += "version/" + version + "/"; + } + url += "browser/"; + return url; } function getGene(dataset, version, gene) { - return $http.get(baseUrl(dataset, version) + "gene/" + gene).then(function(data) { + return $http.get(baseUrl(dataset, version) + "gene/" + gene).then(function(data) { return data.data; }); } @@ -41,9 +41,9 @@ } function getVariant(dataset, version, variant) { - return $http.get(baseUrl(dataset, version) + "variant/" + variant).then(function(data) { + return $http.get(baseUrl(dataset, version) + "variant/" + variant).then(function(data) { return data.data; - }); + }); } function search(dataset, version, query) { diff --git a/scripts/add_picture_to_db.py b/scripts/add_picture_to_db.py index 819c11732..3b6f6eb4b 100755 --- a/scripts/add_picture_to_db.py +++ b/scripts/add_picture_to_db.py @@ -30,18 +30,16 @@ def add_image(dataset_pk, image): data = f.read() try: - mimetype = infer_mimetype( image ) + mimetype = infer_mimetype(image) except NoMimetypeException: print("Can't find mime type for <{}>".format(image)) sys.exit(2) print(len(data)) with db.database.atomic(): - db.DatasetLogo.create( - dataset = dataset, - mimetype = mimetype, - data = data - ) + db.DatasetLogo.create(dataset=dataset, + mimetype=mimetype, + data=data) if __name__ == '__main__': parser = argparse.ArgumentParser(description='Insert a picture into the database') diff --git a/scripts/checkRequests.py b/scripts/checkRequests.py index 40a66ad0b..bbb570fa3 100644 --- a/scripts/checkRequests.py +++ b/scripts/checkRequests.py @@ -1,28 +1,29 @@ from email.mime.multipart import MIMEMultipart from email.mime.text import MIMEText import logging -import peewee +import secrets import smtplib +import peewee + import db -import secrets def send_email(): - msg = MIMEMultipart() - msg['to'] = secrets.admin_address - msg['from'] = secrets.from_address - msg['subject'] = 'Pending SweFreq requests' - msg['reply-to'] = secrets.reply_to_address - body = "There are pending requests for SweFreq accounts, please visit http://swefreq.nbis.se" + msg = MIMEMultipart() + msg['to'] = secrets.admin_address # pylint: disable=no-member + msg['from'] = secrets.from_address # pylint: disable=no-member + msg['subject'] = 'Pending SweFreq requests' + msg['reply-to'] = secrets.reply_to_address # pylint: disable=no-member + body = "There are pending requests for SweFreq accounts, please visit http://swefreq.nbis.se" msg.attach(MIMEText(body, 'plain')) - server = smtplib.SMTP(secrets.mail_server) + server = smtplib.SMTP(secrets.mail_server) # pylint: disable=no-member server.sendmail(msg['from'], [msg['to']], msg.as_string()) if __name__ == '__main__': requests = db.get_outstanding_requests(1) try: - requests.get() # There's at least one request + requests.get() # There's at least one request send_email() except peewee.DoesNotExist: # No new users so we don't send any emails. diff --git a/scripts/compile_template.py b/scripts/compile_template.py index 1955ac6da..49049c93e 100644 --- a/scripts/compile_template.py +++ b/scripts/compile_template.py @@ -1,37 +1,37 @@ -import jinja2 import argparse import datetime from pathlib import Path -class Jinja2Renderer(object): +import jinja2 + +class Jinja2Renderer: def __init__(self, directory): - self.env = jinja2.Environment( - autoescape = True, - block_start_string = '[%', - block_end_string = '%]', - variable_start_string = '[[', - variable_end_string = ']]', - comment_start_string = '[#', - comment_end_string = '#]', - - loader=jinja2.FileSystemLoader( str(directory) ) - ) + self.env = jinja2.Environment(autoescape=True, + block_start_string='[%', + block_end_string='%]', + variable_start_string='[[', + variable_end_string=']]', + comment_start_string='[#', + comment_end_string='#]', + loader=jinja2.FileSystemLoader(str(directory))) def render(self, file, **kwargs): - template = self.env.get_template( str(file) ) - return template.render( **kwargs ) + template = self.env.get_template(str(file)) + return template.render(**kwargs) def main(): parser = argparse.ArgumentParser() parser.add_argument("-b", "--basedir", dest='basedir', required=True) - parser.add_argument("-s", "--source", dest='src', required=True) + parser.add_argument("-s", "--source", dest='src', required=True) parser.add_argument("-d", "--develop", dest='develop', required=False, action='store_true') args = parser.parse_args() - src = Path(args.src).relative_to( args.basedir ) + src = Path(args.src).relative_to(args.basedir) renderer = Jinja2Renderer(args.basedir) - res = renderer.render( src, develop = args.develop, version=datetime.datetime.now().strftime("%Y%m%d%H%M%S.%f") ) + res = renderer.render(src, + develop=args.develop, + version=datetime.datetime.now().strftime("%Y%m%d%H%M%S.%f")) print(res) diff --git a/scripts/importer/data_importer/data_importer.py b/scripts/importer/data_importer/data_importer.py index 4d61dfbaf..85fb8ea48 100644 --- a/scripts/importer/data_importer/data_importer.py +++ b/scripts/importer/data_importer/data_importer.py @@ -26,7 +26,7 @@ def __init__(self, settings): self.progress_bar = not settings.disable_progress self.in_file = None - def _connect(self, host, user, passwd, database): + def _connect(self, host, user, passwd, database): # pylint: disable=no-self-use try: logging.info("Connecting to database {}".format(database)) database = MySQLdb.connect(host=host, @@ -34,7 +34,7 @@ def _connect(self, host, user, passwd, database): passwd=passwd, db=database) return database.cursor() - except MySQLdb.Error as error: + except MySQLdb.Error as error: # pylint: disable=no-member logging.error("Error connecting: {}".format(error)) def _download(self, base_url, version=None): @@ -87,16 +87,18 @@ def _download_and_open(self, base_url, version=None): filename = self._download(base_url, version) return self._open(filename) - def _open(self, filename, binary=True): + def _open(self, filename, binary=True): # pylint: disable=no-self-use mode = 'rb' if binary else 'rt' encoding = None if binary else 'utf8' try: logging.debug("Opening file {}".format(filename)) - return gzip.open(filename, mode, encoding=encoding) if filename.endswith(".gz") else open(filename) + return gzip.open(filename, mode, encoding=encoding) \ + if filename.endswith(".gz") \ + else open(filename) except IOError as error: logging.error("IOERROR: {}".format(error)) - def _time_format(self, seconds): + def _time_format(self, seconds): # pylint: disable=no-self-use hour, rem = divmod(seconds, 3600) mins, secs = divmod(rem, 60) retval = "" @@ -113,7 +115,7 @@ def _time_since(self, start): def _time_to(self, start, progress=0.01): return self._time_format((time.time() - start)/progress) - def _update_progress_bar(self, current_count, total, last_progress, finished=False): + def _update_progress_bar(self, current_count, total, last_progress, finished=False): # pylint: disable=no-self-use if not finished: progress = current_count/total else: diff --git a/scripts/importer/data_importer/old_db.py b/scripts/importer/data_importer/old_db.py deleted file mode 100644 index 7decaf19d..000000000 --- a/scripts/importer/data_importer/old_db.py +++ /dev/null @@ -1,303 +0,0 @@ -from peewee import ( - BlobField, - CharField, - DateTimeField, - Field, - FloatField, - ForeignKeyField, - IntegerField, - Model, - MySQLDatabase, - PrimaryKeyField, - TextField, - fn, - ) -import settings - -mysql_database = MySQLDatabase( - settings.mysql_schema, - host=settings.mysql_host, - user=settings.mysql_user, - password=settings.mysql_passwd, - port=settings.mysql_port - ) - - -class MySQLModel(Model): - class Meta: - database = mysql_database - - -class EnumField(Field): - db_field = 'string' # The same as for CharField - - def __init__(self, values=None, *args, **kwargs): - self.values = values or [] - super().__init__(*args, **kwargs) - - def db_value(self, value): - if value not in self.values: - raise ValueError("Illegal value for '{}'".format(self.db_column)) - return value - - def python_value(self, value): - if value not in self.values: - raise ValueError("Illegal value for '{}'".format(self.db_column)) - return value - - -class User(MySQLModel): - user = PrimaryKeyField(db_column='user_pk') - name = CharField(null=True) - email = CharField(unique=True) - identity = CharField(unique=True) - identity_type = EnumField(null=False, values=['google', 'elixir']) - affiliation = CharField(null=True) - country = CharField(null=True) - - def is_admin(self, dataset): - return (DatasetAccess.select() - .where(DatasetAccess.dataset == dataset, - DatasetAccess.user == self, - DatasetAccess.is_admin) - .count()) - - def has_access(self, dataset): - return DatasetAccessCurrent.select().where( - DatasetAccessCurrent.dataset == dataset, - DatasetAccessCurrent.user == self, - ).count() - - def has_requested_access(self, dataset): - return DatasetAccessPending.select().where( - DatasetAccessPending.dataset == dataset, - DatasetAccessPending.user == self - ).count() - - class Meta: - db_table = 'user' - - -class Study(MySQLModel): - study = PrimaryKeyField(db_column='study_pk') - pi_name = CharField() - pi_email = CharField() - contact_name = CharField() - contact_email = CharField() - title = CharField() - description = TextField(null=True) - publication_date = DateTimeField() - ref_doi = CharField(null=True) - - class Meta: - db_table = 'study' - - -class Dataset(MySQLModel): - dataset = PrimaryKeyField(db_column='dataset_pk') - study = ForeignKeyField(Study, db_column='study_pk', to_field='study', related_name='datasets') - short_name = CharField() - full_name = CharField() - browser_uri = CharField(null=True) - beacon_uri = CharField(null=True) - avg_seq_depth = FloatField(null=True) - seq_type = CharField(null=True) - seq_tech = CharField(null=True) - seq_center = CharField(null=True) - dataset_size = IntegerField() - mongodb_collection = CharField(null=False) - - def has_image(self): - try: - DatasetLogo.get(DatasetLogo.dataset == self) - return True - except DatasetLogo.DoesNotExist: - return False - - class Meta: - db_table = 'dataset' - - -class DatasetVersion(MySQLModel): - dataset_version = PrimaryKeyField(db_column='dataset_version_pk') - dataset = ForeignKeyField(Dataset, db_column='dataset_pk', to_field='dataset', related_name='versions') - version = CharField() - description = TextField() - terms = TextField() - var_call_ref = CharField(null=True) - available_from = DateTimeField() - ref_doi = CharField(null=True) - data_contact_name = CharField(null=True) - data_contact_link = CharField(null=True) - - class Meta: - db_table = 'dataset_version' - - -class Collection(MySQLModel): - collection = PrimaryKeyField(db_column = 'collection_pk') - name = CharField(null = True) - ethnicity = CharField(null = True) - - class Meta: - db_table = 'collection' - - -class SampleSet(MySQLModel): - sample_set = PrimaryKeyField(db_column='sample_set_pk') - dataset = ForeignKeyField(Dataset, db_column='dataset_pk', to_field='dataset', related_name='sample_sets') - collection = ForeignKeyField(Collection, db_column='collection_pk', to_field='collection', related_name='sample_sets') - sample_size = IntegerField() - phenotype = CharField(null=True) - - class Meta: - db_table = 'sample_set' - - -class DatasetFile(MySQLModel): - dataset_file = PrimaryKeyField(db_column='dataset_file_pk') - dataset_version = ForeignKeyField(DatasetVersion, db_column='dataset_version_pk', to_field='dataset_version', related_name='files') - name = CharField() - uri = CharField() - bytes = IntegerField() - - class Meta: - db_table = 'dataset_file' - - -class UserAccessLog(MySQLModel): - user_access_log = PrimaryKeyField(db_column='user_access_log_pk') - user = ForeignKeyField(User, db_column='user_pk', to_field='user', related_name='access_logs') - dataset = ForeignKeyField(Dataset, db_column='dataset_pk', to_field='dataset', related_name='access_logs') - action = EnumField(null=True, values=['access_requested','access_granted','access_revoked','private_link']) - ts = DateTimeField() - - class Meta: - db_table = 'user_access_log' - - -class UserConsentLog(MySQLModel): - user_consent_log = PrimaryKeyField(db_column='user_consent_log_pk') - user = ForeignKeyField(User, db_column='user_pk', to_field='user', related_name='consent_logs') - dataset_version = ForeignKeyField(DatasetVersion, db_column='dataset_version_pk', to_field='dataset_version', related_name='consent_logs') - ts = DateTimeField() - - class Meta: - db_table = 'user_consent_log' - - -class UserDownloadLog(MySQLModel): - user_download_log = PrimaryKeyField(db_column='user_download_log_pk') - user = ForeignKeyField(User, db_column='user_pk', to_field='user', related_name='download_logs') - dataset_file = ForeignKeyField(DatasetFile, db_column='dataset_file_pk', to_field='dataset_file', related_name='download_logs') - ts = DateTimeField() - - class Meta: - db_table = 'user_download_log' - - -class DatasetAccess(MySQLModel): - dataset_access = PrimaryKeyField(db_column='dataset_access_pk') - dataset = ForeignKeyField(Dataset, db_column='dataset_pk', to_field='dataset', related_name='access') - user = ForeignKeyField(User, db_column='user_pk', to_field='user', related_name='access') - wants_newsletter = IntegerField(null=True) - is_admin = IntegerField(null=True) - - class Meta: - db_table = 'dataset_access' - - -class DatasetAccessCurrent(DatasetAccess): - dataset = ForeignKeyField(Dataset, db_column='dataset_pk', to_field='dataset', related_name='access_current') - user = ForeignKeyField(User, db_column='user_pk', to_field='user', related_name='access_current') - has_access = IntegerField() - access_requested = DateTimeField() - - class Meta: - db_table = 'dataset_access_current' - - -class DatasetAccessPending(DatasetAccess): - dataset = ForeignKeyField(Dataset, db_column='dataset_pk', to_field='dataset', related_name='access_pending') - user = ForeignKeyField(User, db_column='user_pk', to_field='user', related_name='access_pending') - has_access = IntegerField() - access_requested = DateTimeField() - - class Meta: - db_table = 'dataset_access_pending' - - -class DatasetLogo(MySQLModel): - dataset_logo = PrimaryKeyField(db_column='dataset_logo_pk') - dataset = ForeignKeyField(Dataset, db_column='dataset_pk', to_field='dataset', related_name='logo') - mimetype = CharField() - data = BlobField() - - class Meta: - db_table = 'dataset_logo' - - -class Linkhash(MySQLModel): - linkhash = PrimaryKeyField(db_column='linkhash_pk') - dataset_version = ForeignKeyField(DatasetVersion, db_column='dataset_version_pk', to_field='dataset_version', related_name='link_hashes') - user = ForeignKeyField(User, db_column='user_pk', to_field='user', related_name='link_hashes') - hash = CharField() - expires_on = DateTimeField() - - class Meta: - db_table = 'linkhash' - - -class DatasetVersionCurrent(DatasetVersion): - dataset = ForeignKeyField(Dataset, db_column='dataset_pk', to_field='dataset', related_name='current_version') - - class Meta: - db_table = 'dataset_version_current' - - -class SFTPUser(MySQLModel): - sftp_user = PrimaryKeyField(db_column='sftp_user_pk') - user = ForeignKeyField(User, db_column='user_pk', to_field='user', related_name='sftp_user') - user_uid = IntegerField(unique=True) - user_name = CharField(null=False) - password_hash = CharField(null=False) - account_expires = DateTimeField(null=False) - - class Meta: - db_table = 'sftp_user' - - -def get_next_free_uid(): - """ - Returns the next free uid >= 10000, and higher than the current uid's - from the sftp_user table in the database. - """ - default = 10000 - next_uid = default - try: - current_max_uid = SFTPUser.select(fn.MAX(SFTPUser.user_uid)).get().user_uid - if current_max_uid: - next_uid = current_max_uid+1 - except SFTPUser.DoesNotExist: - pass - - return next_uid - - -def get_admin_datasets(user): - return DatasetAccess.select().where( DatasetAccess.user == user, DatasetAccess.is_admin) - - -def get_dataset(dataset): - dataset = Dataset.select().where( Dataset.short_name == dataset).get() - return dataset - - -def build_dict_from_row(row): - d = {} - for field in row._meta.sorted_fields: #pylint: disable=protected-access - column = field.db_column - if column.endswith("_pk"): - continue - d[column] = getattr(row, column) - return d diff --git a/scripts/importer/data_importer/old_db_importer.py b/scripts/importer/data_importer/old_db_importer.py deleted file mode 100644 index a1beb077c..000000000 --- a/scripts/importer/data_importer/old_db_importer.py +++ /dev/null @@ -1,447 +0,0 @@ -#!/usr/bin/env python3 - -import sys -import time -import logging -import db -from peewee import OperationalError, InterfaceError -from . import old_db - -from .data_importer import DataImporter - -class OldDbImporter( DataImporter ): - - def __init__(self, settings): - super().__init__(settings) - self.reference_sets = [] - self.id_map = {'collection':{}, - 'study':{}, - 'dataset':{}, - 'dataset_version':{}, - 'dataset_file':{}, - 'user':{} - } - - def _select_reference_set(self, short_name): - if len(self.reference_sets) == 1: - logging.info(("Only one reference set is available, %s, " - "will default to this set for all datasets"), - self.reference_sets[0].name) - return self.reference_sets[0].id - elif short_name.lower() in [r.name.lower() for r in self.reference_sets]: - refset = [r for r in self.reference_sets if r.name.lower() == short_name.lower()][0] - logging.info("Auto-selecting reference set '%s' based on name.", refset.name) - return refset - else: - print("Select a reference set to use with this dataset") - retval = -1 - while retval not in [r.id for r in self.reference_sets]: - for reference_set in self.reference_sets: - print(" {} : {}".format(reference_set.id, reference_set.name)) - try: - retval = int(input("Please select a reference: ")) - except ValueError: - print("Please select a number in {}".format([r.id for r in self.reference_sets])) - return retval - - def _move_collections(self): - logging.info("Moving Collections") - for collection in old_db.Collection.select(): - logging.info(" - Moving '{}'".format(collection.name)) - - try: - new_id = db.Collection.get(name = collection.name, - ethnicity = collection.ethnicity).id - except db.Collection.DoesNotExist: - if self.settings.dry_run: - continue - new_id = (db.Collection - .insert(name = collection.name, - ethnicity = collection.ethnicity) - .execute()) - - self.id_map['collection'][collection.collection] = new_id - - def _move_studies(self): - logging.info("Moving Studies") - for study in old_db.Study.select(): - logging.info(" - Moving '{}'".format(study.title)) - - try: - new_id = db.Study.get(pi_name = study.pi_name, - pi_email = study.pi_email, - contact_name = study.contact_name, - contact_email = study.contact_email, - title = study.title, - description = study.description, - publication_date = study.publication_date, - ref_doi = study.ref_doi).id - except db.Study.DoesNotExist: - if self.settings.dry_run: - continue - new_id = (db.Study - .insert(pi_name = study.pi_name, - pi_email = study.pi_email, - contact_name = study.contact_name, - contact_email = study.contact_email, - title = study.title, - description = study.description, - publication_date = study.publication_date, - ref_doi = study.ref_doi) - .execute()) - - self.id_map['study'][study.study] = new_id - - def _move_datasets(self): - logging.info("Moving Datasets") - for dataset in old_db.Dataset.select(): - logging.info(" - Moving '{}'".format(dataset.short_name)) - try: - study_ref_id = self.id_map['study'][dataset.study.study] - except KeyError: - if not self.settings.dry_run: - raise - study_ref_id = -1 - try: - # short_name is unique, so we only really need to check that. - new_id = db.Dataset.get(study = study_ref_id, - short_name = dataset.short_name).id - except db.Dataset.DoesNotExist: - if self.settings.dry_run: - continue - new_id = (db.Dataset - .insert(study = study_ref_id, - short_name = dataset.short_name, - full_name = dataset.full_name, - browser_uri = dataset.browser_uri, - beacon_uri = dataset.beacon_uri, - avg_seq_depth = dataset.avg_seq_depth, - seq_type = dataset.seq_type, - seq_tech = dataset.seq_tech, - seq_center = dataset.seq_center, - dataset_size = dataset.dataset_size) - .execute()) - - self.id_map['dataset'][dataset.dataset] = new_id - - def _move_dataset_logos(self): - logging.info("Moving Dataset Logos") - for dataset_file in old_db.DatasetLogo.select(): - try: - dataset_ref_id = self.id_map['dataset'][dataset_file.dataset.dataset] - except KeyError: - if not self.settings.dry_run: - raise - dataset_ref_id = -1 - try: - db.DatasetLogo.get(dataset = dataset_ref_id, - mimetype = dataset_file.mimetype, - data = dataset_file.data) - except db.DatasetLogo.DoesNotExist: - if self.settings.dry_run: - continue - db.DatasetLogo.insert(dataset = dataset_ref_id, - mimetype = dataset_file.mimetype, - data = dataset_file.data).execute() - - def _move_dataset_versions(self): - logging.info("Moving Dataset Versions") - for dataset_version in old_db.DatasetVersion.select(): - try: - dataset_ref_id = self.id_map['dataset'][dataset_version.dataset.dataset] - dataset = db.Dataset.get(id = dataset_ref_id) - except KeyError: - if not self.settings.dry_run: - raise - dataset_ref_id = -1 - try: - new_id = db.DatasetVersion.get(dataset = dataset_ref_id, - version = dataset_version.version, - description = dataset_version.description, - terms = dataset_version.terms, - var_call_ref = dataset_version.var_call_ref, - available_from = dataset_version.available_from, - ref_doi = dataset_version.ref_doi, - data_contact_name = dataset_version.data_contact_name, - data_contact_link = dataset_version.data_contact_link).id - except db.DatasetVersion.DoesNotExist: - target_reference_id = self._select_reference_set(dataset.short_name) - if self.settings.dry_run: - continue - new_id = (db.DatasetVersion - .insert(dataset = dataset_ref_id, - reference_set = target_reference_id, - version = dataset_version.version, - description = dataset_version.description, - terms = dataset_version.terms, - var_call_ref = dataset_version.var_call_ref, - available_from = dataset_version.available_from, - ref_doi = dataset_version.ref_doi, - data_contact_name = dataset_version.data_contact_name, - data_contact_link = dataset_version.data_contact_link, - coverage_levels = [1,5,10,15,20,25,30,50,100] - ) - .execute()) - - self.id_map['dataset_version'][dataset_version.dataset_version] = new_id - - def _move_dataset_files(self): - logging.info("Moving Dataset Files") - for dataset_file in old_db.DatasetFile.select(): - logging.info(" - Moving '{}'".format(dataset_file.name)) - try: - dataset_version_ref_id = self.id_map['dataset_version'][dataset_file.dataset_version.dataset_version] - except KeyError: - if not self.settings.dry_run: - raise - dataset_version_ref_id = -1 - try: - new_id = db.DatasetFile.get(dataset_version = dataset_version_ref_id, - name = dataset_file.name, - uri = dataset_file.uri, - file_size = dataset_file.bytes).id - except db.DatasetFile.DoesNotExist: - if self.settings.dry_run: - continue - new_id = (db.DatasetFile - .insert(dataset_version = dataset_version_ref_id, - name = dataset_file.name, - uri = dataset_file.uri, - file_size = dataset_file.bytes).execute()) - - self.id_map['dataset_file'][dataset_file.dataset_file] = new_id - - def _move_sample_sets(self): - logging.info("Moving Sample Sets") - for sample_set in old_db.SampleSet.select(): - try: - dataset_ref_id = self.id_map['dataset'][sample_set.dataset.dataset] - collection_ref_id = self.id_map['collection'][sample_set.collection.collection] - except KeyError: - if not self.settings.dry_run: - raise - dataset_ref_id = -1 - collection_ref_id = -1 - try: - db.SampleSet.get(dataset = dataset_ref_id, - collection = collection_ref_id, - sample_size = sample_set.sample_size, - phenotype = sample_set.phenotype) - except db.SampleSet.DoesNotExist: - if self.settings.dry_run: - continue - db.SampleSet.insert(dataset = dataset_ref_id, - collection = collection_ref_id, - sample_size = sample_set.sample_size, - phenotype = sample_set.phenotype).execute() - - def _move_database(self): - self._move_collections() - self._move_studies() - self._move_datasets() - self._move_dataset_logos() - self._move_dataset_versions() - self._move_sample_sets() - self._move_dataset_files() - - def _move_users(self): - logging.info("Moving Users") - for user in old_db.User.select(): - try: - new_id = (db.User - .get(name = user.name, - email = user.email, - identity = user.identity, - identity_type = user.identity_type, - affiliation = user.affiliation, - country = user.country).id) - except db.User.DoesNotExist: - if self.settings.dry_run: - continue - new_id = (db.User - .insert(name = user.name, - email = user.email, - identity = user.identity, - identity_type = user.identity_type, - affiliation = user.affiliation, - country = user.country).execute()) - - self.id_map['user'][user.user] = new_id - - def _move_sftp_users(self): - logging.info("Moving SFTP Users") - for user in old_db.SFTPUser.select(): - try: - user_ref_id = self.id_map['user'][user.user.user] - except KeyError: - if not self.settings.dry_run: - raise - user_ref_id = -1 - try: - # user_uid is unique, so we rely on that - db.SFTPUser.get(user = user_ref_id, - user_uid = user.user_uid) - except db.SFTPUser.DoesNotExist: - if self.settings.dry_run: - continue - db.SFTPUser.insert(user = user_ref_id, - user_uid = user.user_uid, - user_name = user.user_name, - password_hash = user.password_hash, - account_expires = user.account_expires).execute() - - def _move_user_access_logs(self): - logging.info("Moving User Access Logs") - for log in old_db.UserAccessLog.select(): - try: - user_ref_id = self.id_map['user'][log.user.user] - dataset_ref_id = self.id_map['dataset'][log.dataset.dataset] - except KeyError: - if not self.settings.dry_run: - raise - user_ref_id = -1 - dataset_ref_id = -1 - try: - db.UserAccessLog.get(user = user_ref_id, - dataset = dataset_ref_id, - action = log.action, - ts = log.ts) - except db.UserAccessLog.DoesNotExist: - if self.settings.dry_run: - continue - db.UserAccessLog.insert(user = user_ref_id, - dataset = dataset_ref_id, - action = log.action, - ts = log.ts).execute() - - def _move_user_consent_logs(self): - logging.info("Moving User Consent Logs") - for log in old_db.UserConsentLog.select(): - try: - user_ref_id = self.id_map['user'][log.user.user] - version_ref_id = self.id_map['dataset_version'][log.dataset_version.dataset_version] - except KeyError: - if not self.settings.dry_run: - raise - user_ref_id = -1 - version_ref_id = -1 - try: - db.UserConsentLog.get(user = user_ref_id, - dataset_version = version_ref_id, - ts = log.ts) - except db.UserConsentLog.DoesNotExist: - if self.settings.dry_run: - continue - db.UserConsentLog.insert(user = user_ref_id, - dataset_version = version_ref_id, - ts = log.ts).execute() - - def _move_user_download_logs(self): - logging.info("Moving User Download Logs") - for log in old_db.UserDownloadLog.select(): - try: - user_ref_id = self.id_map['user'][log.user.user] - file_ref_id = self.id_map['dataset_file'][log.dataset_file.dataset_file] - except KeyError: - if not self.settings.dry_run: - raise - user_ref_id = -1 - file_ref_id = -1 - try: - db.UserDownloadLog.get(user = user_ref_id, - dataset_file = file_ref_id, - ts = log.ts) - except db.UserDownloadLog.DoesNotExist: - if self.settings.dry_run: - continue - db.UserDownloadLog.insert(user = user_ref_id, - dataset_file = file_ref_id, - ts = log.ts).execute() - - def _move_dataset_access(self): - logging.info("Moving Dataset Access Records") - for access in old_db.DatasetAccess.select(): - try: - user_ref_id = self.id_map['user'][access.user.user] - dataset_ref_id = self.id_map['dataset'][access.dataset.dataset] - except KeyError: - if not self.settings.dry_run: - raise - user_ref_id = -1 - dataset_ref_id = -1 - try: - db.DatasetAccess.get(dataset = dataset_ref_id, - user = user_ref_id, - wants_newsletter = access.wants_newsletter, - is_admin = access.is_admin) - except db.DatasetAccess.DoesNotExist: - if self.settings.dry_run: - continue - db.DatasetAccess.insert(dataset = dataset_ref_id, - user = user_ref_id, - wants_newsletter = access.wants_newsletter, - is_admin = access.is_admin).execute() - - def _move_linkhashes(self): - logging.info("Moving Linkhashes") - for linkhash in old_db.Linkhash.select(): - try: - user_ref_id = self.id_map['user'][linkhash.user.user] - version_ref_id = self.id_map['dataset_version'][linkhash.dataset_version.dataset_version] - except KeyError: - if not self.settings.dry_run: - raise - user_ref_id = -1 - version_ref_id = -1 - try: - db.Linkhash.get(dataset_version = version_ref_id, - user = user_ref_id, - hash = linkhash.hash, - expires_on = linkhash.expires_on) - except db.Linkhash.DoesNotExist: - if self.settings.dry_run: - continue - db.Linkhash.insert(dataset_version = version_ref_id, - user = user_ref_id, - hash = linkhash.hash, - expires_on = linkhash.expires_on).execute() - - def _move_userbase(self): - self._move_users() - self._move_sftp_users() - self._move_user_access_logs() - self._move_user_consent_logs() - self._move_user_download_logs() - self._move_dataset_access() - self._move_linkhashes() - - def prepare_data(self): - """ - Connects to the old and new databases. - """ - logging.info("Checking connection to old database") - try: - old_db.Collection.get() - except OperationalError: - logging.error("Could not connect to old database") - sys.exit(1) - logging.info("Checking connection to new database") - try: - db.ReferenceSet.get() - for reference_set in db.ReferenceSet.select(): - self.reference_sets += [reference_set] - except db.ReferenceSet.DoesNotExist: - logging.error(("Connection works, but no reference sets are available." - "use '--add_reference' to add a new reference set and" - "Then use this tool again.")) - sys.exit(1) - except (OperationalError, InterfaceError): - logging.error("Could not connect to new database") - sys.exit(1) - - def start_import(self): - start = time.time() - self._move_database() - self._move_userbase() - - logging.info("Moved data in {}".format(self._time_since(start))) diff --git a/scripts/importer/data_importer/raw_data_importer.py b/scripts/importer/data_importer/raw_data_importer.py index b1594b04a..3c8c0cc99 100644 --- a/scripts/importer/data_importer/raw_data_importer.py +++ b/scripts/importer/data_importer/raw_data_importer.py @@ -1,4 +1,6 @@ #!/usr/bin/env python3 +"""Read data from a vcf file and add the variants to a database.""" + import re import sys import time @@ -22,7 +24,10 @@ class RawDataImporter(DataImporter): + """Read data from a vcf file and add the variants to a database.""" + def __init__(self, settings): + """Set the provided settings and prepare the main variables.""" super().__init__(settings) self.dataset_version = None self.dataset = None @@ -36,7 +41,7 @@ def __init__(self, settings): self.chrom = None def _set_dataset_info(self): - """ Save dataset information given as parameters """ + """Save dataset information given as parameters.""" if self.settings.beacon_description: self.dataset.description = self.settings.beacon_description self.dataset.save() @@ -51,31 +56,32 @@ def _set_dataset_info(self): self.dataset.save() def _select_dataset_version(self): - datasets = [] - + """Select the dataset version to use.""" # Make sure that the dataset exists try: - ds = db.Dataset.get(short_name=self.settings.dataset) + chosen_ds = db.Dataset.get(short_name=self.settings.dataset) except db.Dataset.DoesNotExist: - logging.error("Unknown dataset '%s'", self.settings.dataset) + logging.error(f"Unknown dataset {self.settings.dataset}") logging.info("Available datasets are:") for dataset in db.Dataset.select(): - logging.info(" * %s", dataset.short_name) + logging.info(f" * {dataset.short_name}") sys.exit(1) - logging.info("Using dataset {}".format(ds.short_name)) - self.dataset = ds + logging.info(f"Using dataset {chosen_ds.short_name}") + self.dataset = chosen_ds - versions = [v for v in db.DatasetVersion.select().where(db.DatasetVersion.dataset == ds)] + versions = [v for v in (db.DatasetVersion.select(). + where(db.DatasetVersion.dataset == chosen_ds))] # Make sure that the dataset version exists if not versions: raise db.DatasetVersion.DoesNotExist("No versions exist for this dataset") if self.settings.version not in [v.version for v in versions]: - logging.error("Unknown version '%s' for dataset '%s'.", self.settings.version, self.dataset.short_name) + logging.error(f"Unknown version '{self.settings.version}' " + + f"for dataset '{self.dataset.short_name}'.") logging.info("Available versions are:") for version in versions: - logging.info(" * %s", version.version) + logging.info(f" * {version.version}") sys.exit(1) self.dataset_version = [v for v in versions if v.version == self.settings.version][0] @@ -92,6 +98,8 @@ def _select_dataset_version(self): def _create_beacon_counts(self): """ + Prepare counts for the beacon. + Add the number of unique references at each position (callcount), the number of unique ref-alt pairs at each position (variantount) and the datasetid (eg GRCh37:swegen:2019-01-01) @@ -108,12 +116,15 @@ def _create_beacon_counts(self): datarow = {'datasetid': datasetid, 'callcount': self.counter['calls'], 'variantcount': self.counter['beaconvariants']} - logging.info('Dataset counts: callcount: %s, variantcount: %s', datarow['callcount'], datarow['variantcount']) + logging.info(f"Dataset counts: callcount: {datarow['callcount']}, " + + f"variantcount: {datarow['variantcount']}") if not self.settings.dry_run: db.BeaconCounts.insert(datarow).execute() def _insert_coverage(self): """ + Import coverage. + Header columns are chromosome, position, mean coverage, median coverage, and then coverage under 1, 5 10, 15, 20, 25, 30, 50, 100. """ @@ -133,11 +144,7 @@ def _insert_coverage(self): if line.startswith("#"): continue - data = {} - for i, item in enumerate(line.strip().split("\t")): - if i == 0: - data['dataset_version'] = self.dataset_version - data[header[i][0]] = header[i][1](item) + data = self._parse_baseinfo(header, line) # re-format coverage for batch data['coverage'] = [data['cov1'], data['cov5'], data['cov10'], @@ -163,130 +170,236 @@ def _insert_coverage(self): batch = [] # Update progress if self.counter['coverage'] is not None: - last_progress = self._update_progress_bar(counter, self.counter['coverage'], last_progress) + last_progress = self._update_progress_bar(counter, + self.counter['coverage'], + last_progress) if batch and not self.settings.dry_run: db.Coverage.insert_many(batch).execute() if self.counter['coverage'] is not None: - last_progress = self._update_progress_bar(counter, self.counter['coverage'], last_progress, finished=True) - self.log_insertion(counter, "coverage", start) + last_progress = self._update_progress_bar(counter, + self.counter['coverage'], + last_progress, + finished=True) + self._log_insertion(counter, "coverage", start) def _parse_manta(self): + """Parse a manta file.""" + # Skip column 5 and 6 (QUAL and FILTER), will not be used header = [("chrom", str), ("pos", int), ("chrom_id", str), ("ref", str), ("alt", str)] batch = [] - samples = 0 counter = 0 + last_progress = 0 start = time.time() for filename in self.settings.variant_file: for line in self._open(filename): line = line.strip() if line.startswith("#"): - if line.startswith('#CHROM'): - samples = len(line.split('\t')[9:]) continue - base = {} - for i, item in enumerate(line.split("\t")): - if i == 0: - base['dataset_version'] = self.dataset_version - if i < 5: - base[header[i][0]] = header[i][1](item) - elif i == 7: - # only parse column 7 (maybe also for non-beacon-import?) - info = dict([(x.split('=', 1)) if '=' in x else (x, x) for x in re.split(';(?=\w)', item)]) + base = self._parse_baseinfo(header, line) + info = self._parse_info(line) if info.get('SVTYPE') != 'BND': continue - if base["chrom"].startswith('GL') or base["chrom"].startswith('MT'): - # A BND from GL or MT. GL is an unplaced scaffold, MT is mitochondria. + if self._is_non_chromosome(base["chrom"]): + # A BND *from* a non-chromosome. continue - if 'NSAMPLES' in info: - # save this unless we already know the sample size - samples = int(info['NSAMPLES']) - - alt_alleles = base['alt'].split(",") - for i, alt in enumerate(alt_alleles): - data = dict(base) - data['allele_freq'] = float(info.get('FRQ')) - data['alt'], data['mate_chrom'], data['mate_start'] = re.search('(.+)[[\]](.*?):(\d+)[[\]]', alt).groups() - if data['mate_chrom'].startswith('GL') or data['mate_chrom'].startswith('MT'): - # A BND from a chromosome to GL or MT. - # TODO ask a bioinformatician if these cases should be included or not - continue - data['mate_id'] = info.get('MATEID', '') - data['variant_id'] = '{}-{}-{}-{}'.format(data['chrom'], data['pos'], data['ref'], alt) - data['allele_count'] = data.get('allele_count', 0) - data['allele_num'] = data.get('allele_num', 0) - batch += [data] - if self.settings.add_reversed_mates: - # If the vcf only contains one line per breakend, add the reversed version to the database here. - reversed = dict(data) - # Note: in general, ref and alt cannot be assumed to be the same in the reversed direction, - # but our data (so far) only contains N, so we just keep them as is for now. - reversed.update({'mate_chrom': data['chrom'], 'chrom': data['mate_chrom'], - 'mate_start': data['pos'], 'pos': data['mate_start'], - 'chrom_id': data['mate_id'], 'mate_id': data['chrom_id']}) - reversed['variant_id'] = '{}-{}-{}-{}'.format(reversed['chrom'], reversed['pos'], reversed['ref'], alt) - counter += 1 # increase the counter; reversed BNDs are usually kept at their own vcf row - batch += [reversed] - - counter += 1 # count variants (one per vcf row) + batch += self._parse_bnd_alleles(base, info) + + # count variants (one per vcf row) + counter += 1 if len(batch) >= self.settings.batch_size: if not self.settings.dry_run: db.VariantMate.insert_many(batch).execute() - batch = [] + # Update progress - if not self.counter['variants']: - last_progress = self._update_progress_bar(counter, self.counter['variants'], last_progress) + if self.counter['variants']: + last_progress = self._update_progress_bar(counter, + self.counter['variants'], + last_progress) + # Store all variants and counter values if batch and not self.settings.dry_run: db.VariantMate.insert_many(batch).execute() - if self.settings.set_vcf_sampleset_size and samples: - self.sampleset.sample_size = samples - self.sampleset.save() + if self.counter['variants']: + last_progress = self._update_progress_bar(counter, + self.counter['variants'], + last_progress, + finished=True) + self._log_insertion(counter, "breakend", start) - self.dataset_version.num_variants = counter - self.dataset_version.save() - if not self.counter['variants']: - last_progress = self._update_progress_bar(counter, self.counter['variants'], last_progress, finished=True) - self.log_insertion(counter, "breakend", start) + def _estimate_variant_lastid(self): # pylint: disable=no-self-use + """ + Return the id of the variant with the highest id. + + Returns 0 if table is empty. + + Returns: + int: id of the variant with highest id or 0 - def _insert_variants(self): """ - Insert variants from a VCF file + try: + return (db.Variant.select(db.Variant.id) + .order_by(db.Variant.id.desc()) + .limit(1) + .get().id) + except db.Variant.DoesNotExist: + return 0 + + def _add_variants_to_db(self, batch: list, genes: list, transcripts: list, references: dict): """ - logging.info("Inserting variants%s", " (dry run)" if self.settings.dry_run else "") - header = [("chrom", str), ("pos", int), ("rsid", str), ("ref", str), - ("alt", str), ("site_quality", float), ("filter_string", str)] + Add variants to db. + + Args: + batch (list): variant data (dict) + genes (list): genes for the variants + transcripts(list): transcripts for the variants + references (dict): reference genes and transcripts + """ + if not self.settings.beacon_only: + curr_id = self._estimate_variant_lastid() + + db.Variant.insert_many(batch).execute() + + # check if the variant dbid estimate is correct, otherwise must check manually + if not self.settings.beacon_only: + last_id = self._estimate_variant_lastid() + if last_id and last_id-curr_id == len(batch): + indexes = list(range(curr_id+1, last_id+1)) + else: + logging.warning("Bad match between ids - slow check") + indexes = [] + for entry in batch: + indexes.append(db.Variant.select(db.Variant.id) + .where(db.Variant.variant_id == entry['variant_id']) + .get().id) + self._add_variant_genes(indexes, genes, references['genes']) + self._add_variant_transcripts(indexes, transcripts, references['transcripts']) + + def _get_genes_transcripts(self): + """ + Retrieve the genes and transcripts for the current dataset version in the form + `{entity: dbid}`. + + Returns: + tuple: (genes, transcripts) + + """ + ref_set = self.dataset_version.reference_set + genes = {gene.gene_id: gene.id + for gene in (db.Gene.select(db.Gene.id, db.Gene.gene_id) + .where(db.Gene.reference_set == ref_set))} + transcripts = {tran.transcript_id: tran.id + for tran in (db.Transcript.select(db.Transcript.id, + db.Transcript.transcript_id) + .join(db.Gene) + .where(db.Gene.reference_set == ref_set))} + return genes, transcripts + + def _parse_variant_row(self, line: str, batch_cont: dict, headers: list, vep_field_names: list): # pylint: disable=too-many-locals + """ + Parse a VCF row for a position (potentially multiple variants). + + Data is added in-place. + + Args: + line (str): the raw text row + batch_cont (dict): should contain batch, genes, transcripts + headers (list): (header, type) + vep_field_names (list): VEP field names + + """ + base = self._parse_baseinfo(headers, line) + info = self._parse_info(line) + + if self._is_non_chromosome(base["chrom"]): + return + + consequence_array = info['CSQ'].split(',') if 'CSQ' in info else [] + + alt_alleles = base['alt'].split(",") + rsids = [int(rsid.strip('rs')) + for rsid in base['rsid'].split(';') + if rsid.startswith('rs')] + if not rsids: + rsids = [None] + + try: + hom_counts = [int(info['AC_Hom'])] + except KeyError: + hom_counts = [] # null is better than 0, as 0 has a meaning + except ValueError: + # multiple variants on same row + hom_counts = [int(count) for count in info['AC_Hom'].split(',')] + + base['orig_alt_alleles'] = [f'{base["chrom"]}-{base["pos"]}-{base["ref"]}-{x}' + for x in alt_alleles] + + for i, alt in enumerate(alt_alleles): + data = dict(base) + data['alt'] = alt + + data['rsid'] = rsids[i] if i < len(rsids) else rsids[-1] + + data['allele_num'] = int((info['AN_Adj'] if 'AN_Adj' in info else info['AN'])) + data['allele_freq'] = None + + data['allele_count'] = int((info['AC_Adj'] if 'AC_Adj' in info + else info['AC']).split(',')[i]) + if 'AF' in info and data['allele_num'] > 0: + data['allele_freq'] = data['allele_count']/data['allele_num'] + + if not self.settings.beacon_only: + annotations = [dict(zip(vep_field_names, x.split('|'))) + for x in consequence_array + if len(vep_field_names) == len(x.split('|'))] + data['vep_annotations'] = [ann for ann in annotations + if int(ann['ALLELE_NUM']) == i + 1] + batch_cont['genes'].append(list({annotation['Gene'] + for annotation in data['vep_annotations'] + if annotation['Gene'][:4] == 'ENSG'})) + batch_cont['transcripts'].append(list({annotation['Feature'] + for annotation in data['vep_annotations'] + if annotation['Feature'][:4] == 'ENST'})) + + data['hom_count'] = hom_counts[i] if hom_counts else None + + data['variant_id'] = '{}-{}-{}-{}'.format(data['chrom'], + data['pos'], + data['ref'], + data['alt']) + data['quality_metrics'] = {x: info[x] for x in METRICS if x in info} + batch_cont['batch'] += [data] + if self.settings.count_calls: + self._get_callcount(data) # count calls (one per reference) + self.counter['beaconvariants'] += 1 # count variants (one/alternate) + + def _insert_variants(self): + """Import variants from a VCF file.""" + logging.info(f"Inserting variants{' (dry run)' if self.settings.dry_run else ''}") start = time.time() - batch = [] - genes = [] - transcripts = [] + headers = [("chrom", str), ("pos", int), ("rsid", str), ("ref", str), + ("alt", str), ("site_quality", float), ("filter_string", str)] + batch_container = {'batch': [], + 'genes': [], + 'transcripts': []} + + vep_field_names = None last_progress = -1.0 counter = 0 samples = 0 - vep_field_names = None - dp_mids = None - gq_mids = None + + references = dict(zip(('genes', 'transcripts'), self._get_genes_transcripts())) + with db.database.atomic(): for filename in self.settings.variant_file: - # Get reference set for the variant - ref_set = self.dataset_version.reference_set - - # Get all genes and transcripts for foreign keys - ref_genes = {gene.gene_id: gene.id for gene in (db.Gene.select(db.Gene.id, db.Gene.gene_id) - .where(db.Gene.reference_set == ref_set))} - ref_transcripts = {tran.transcript_id: tran.id for tran in (db.Transcript - .select(db.Transcript.id, - db.Transcript.transcript_id) - .join(db.Gene) - .where(db.Gene.reference_set == ref_set))} for line in self._open(filename, binary=False): line = line.strip() @@ -294,144 +407,39 @@ def _insert_variants(self): # Check for some information that we need if line.startswith('##INFO=').split('|') - if line.startswith('##INFO=').split('|')) - if line.startswith('##INFO=').split('|')) if line.startswith('#CHROM'): samples = len(line.split('\t')[9:]) continue - if not self.settings.beacon_only: - if vep_field_names is None: - logging.error("VEP_field_names is empty. Make sure VCF header is present.") - sys.exit(1) - - base = {} - for i, item in enumerate(line.strip().split("\t")): - if i == 0: - base['dataset_version'] = self.dataset_version - if i < 7: - base[header[i][0]] = header[i][1](item) - elif i == 7 or not self.settings.beacon_only: - # only parse column 7 (maybe also for non-beacon-import?) - info = dict([(x.split('=', 1)) if '=' in x else (x, x) for x in re.split(';(?=\w)', item)]) - - if base["chrom"].startswith('GL') or base["chrom"].startswith('MT'): - continue + if not self.settings.beacon_only and not vep_field_names: + logging.error("VEP_field_names is empty. " + + "Make sure VCF header is present.") + sys.exit(1) - consequence_array = info['CSQ'].split(',') if 'CSQ' in info else [] - if not self.settings.beacon_only: - annotations = [dict(zip(vep_field_names, x.split('|'))) for x in consequence_array if len(vep_field_names) == len(x.split('|'))] - - alt_alleles = base['alt'].split(",") - rsids = [int(rsid.strip('rs')) for rsid in base['rsid'].split(';') if rsid.startswith('rs')] - if not rsids: - rsids = [None] - - try: - hom_counts = [int(info['AC_Hom'])] - except KeyError: - hom_counts = None # null is better than 0, as 0 has a meaning - except ValueError: - hom_counts = [int(count) for count in info['AC_Hom'].split(',')] - - fmt_alleles = [f'{base["chrom"]}-{base["pos"]}-{base["ref"]}-{x}' for x in alt_alleles] - - for i, alt in enumerate(alt_alleles): - if not self.settings.beacon_only: - vep_annotations = [ann for ann in annotations if int(ann['ALLELE_NUM']) == i + 1] - - data = dict(base) - data['pos'], data['ref'], data['alt'] = base['pos'], base['ref'], alt - data['orig_alt_alleles'] = fmt_alleles - - if len(rsids) <= i: - data['rsid'] = rsids[-1] # same id as the last alternate - else: - data['rsid'] = rsids[i] - - an, ac = 'AN_Adj', 'AC_Adj' - if 'AN_Adj' not in info: - an = 'AN' - if 'AC_Adj' not in info: - ac = 'AC' - - data['allele_num'] = int(info[an]) - data['allele_freq'] = None - if 'NS' in info and not samples: - # save this unless we already know the sample size - samples = int(info['NS']) - - data['allele_count'] = int(info[ac].split(',')[i]) - if 'AF' in info and data['allele_num'] > 0: - data['allele_freq'] = data['allele_count']/float(info[an]) - - if not self.settings.beacon_only: - data['vep_annotations'] = vep_annotations - - genes.append(list(set({annotation['Gene'] for annotation in vep_annotations if annotation['Gene'][:4] == 'ENSG'}))) - transcripts.append(list(set({annotation['Feature'] for annotation in vep_annotations if annotation['Feature'][:4] == 'ENST'}))) - - data['hom_count'] = hom_counts[i] if hom_counts else None - - data['variant_id'] = '{}-{}-{}-{}'.format(data['chrom'], data['pos'], data['ref'], data['alt']) - data['quality_metrics'] = dict([(x, info[x]) for x in METRICS if x in info]) - batch += [data] - if self.settings.count_calls: - self.get_callcount(data) # count calls (one per reference) - self.counter['beaconvariants'] += 1 # count variants (one per alternate) + self._parse_variant_row(line, batch_container, headers, vep_field_names) counter += 1 # count variants (one per vcf row) - if len(batch) >= self.settings.batch_size: + if len(batch_container['batch']) >= self.settings.batch_size: if not self.settings.dry_run: - if not self.settings.beacon_only: - try: - curr_id = db.Variant.select(db.Variant.id).order_by(db.Variant.id.desc()).limit(1).get().id - except db.Variant.DoesNotExist: - # assumes next id will be 1 if table is empty - curr_id = 0 - - db.Variant.insert_many(batch).execute() - - if not self.settings.beacon_only: - last_id = db.Variant.select(db.Variant.id).order_by(db.Variant.id.desc()).limit(1).get().id - if last_id-curr_id == len(batch): - indexes = list(range(curr_id+1, last_id+1)) - else: - indexes = [] - for entry in batch: - indexes.append(db.Variant.select(db.Variant.id).where(db.Variant.variant_id == entry['variant_id']).get().id) - self.add_variant_genes(indexes, genes, ref_genes) - self.add_variant_transcripts(indexes, transcripts, ref_transcripts) - - genes = [] - transcripts = [] - batch = [] + self._add_variants_to_db(batch_container['batch'], + batch_container['genes'], + batch_container['transcripts'], + references) + + batch_container['genes'] = [] + batch_container['transcripts'] = [] + batch_container['batch'] = [] # Update progress - if self.counter['variants'] != None: - last_progress = self._update_progress_bar(counter, self.counter['variants'], last_progress) + if self.counter['variants'] is not None: + last_progress = self._update_progress_bar(counter, + self.counter['variants'], + last_progress) - if batch and not self.settings.dry_run: - if not self.settings.beacon_only: - try: - curr_id = db.Variant.select(db.Variant.id).order_by(db.Variant.id.desc()).limit(1).get().id - except db.Variant.DoesNotExist: - # assumes next id will be 1 if table is empty - curr_id = 0 - - db.Variant.insert_many(batch).execute() - - if not self.settings.beacon_only: - last_id = db.Variant.select(db.Variant.id).order_by(db.Variant.id.desc()).limit(1).get().id - if last_id-curr_id == len(batch): - indexes = list(range(curr_id+1, last_id+1)) - else: - indexes = [] - for entry in batch: - indexes.append(db.Variant.select(db.Variant.id).where(db.Variant.variant_id == entry['variant_id']).get().id) - self.add_variant_genes(indexes, genes, ref_genes) - self.add_variant_transcripts(indexes, transcripts, ref_transcripts) + if batch_container['batch'] and not self.settings.dry_run: + self._add_variants_to_db(batch_container['batch'], + batch_container['genes'], + batch_container['transcripts'], + references) if self.settings.set_vcf_sampleset_size and samples: self.sampleset.sample_size = samples @@ -439,17 +447,21 @@ def _insert_variants(self): self.dataset_version.num_variants = counter self.dataset_version.save() - if self.counter['variants'] != None: - last_progress = self._update_progress_bar(counter, self.counter['variants'], last_progress, finished=True) + if self.counter['variants'] is not None: + last_progress = self._update_progress_bar(counter, + self.counter['variants'], + last_progress, + finished=True) - self.log_insertion(counter, "variant", start) + self._log_insertion(counter, "variant", start) - def get_callcount(self, data): + def _get_callcount(self, data): """Increment the call count by the calls found at this position.""" if data['chrom'] == self.chrom and data['pos'] < self.lastpos: # If this position is smaller than the last, the file order might be invalid. # Give a warning, but keep on counting. - msg = "VCF file not ok, variants not given in incremental order. Callcount may not be valid!!!\n\n" + msg = ("VCF file not ok, variants not given in incremental order." + + "Callcount may not be valid!\n\n") logging.warning(msg) if data['chrom'] != self.chrom or data['pos'] != self.lastpos: @@ -465,6 +477,7 @@ def get_callcount(self, data): self.counter['tmp_calls'].add(data['ref']) def count_entries(self): + """Count the number of entries.""" start = time.time() if self.settings.coverage_file: self.counter['coverage'] = 0 @@ -475,7 +488,7 @@ def count_entries(self): if line.startswith("#"): continue self.counter['coverage'] += 1 - logging.info("Found {:,} coverage lines".format(self.counter['coverage'])) + logging.info(f"Found {self.counter['coverage']:,} coverage lines") if self.settings.variant_file: self.counter['variants'] = 0 @@ -491,14 +504,16 @@ def count_entries(self): logging.info("Counted input data lines in {} ".format(self._time_since(start))) def prepare_data(self): + """Prepare for inserting data into db.""" self._select_dataset_version() def start_import(self): + """Start importing data.""" self._set_dataset_info() if self.settings.add_mates: self._parse_manta() if self.settings.count_calls: - logging.warning('Do not know how to count calls in the manta file. Skipping this...') + logging.warning('Cannot count calls in the manta file. Skipping this...') elif self.settings.variant_file: self._insert_variants() if self.settings.count_calls: @@ -506,23 +521,129 @@ def start_import(self): if not self.settings.beacon_only and self.settings.coverage_file: self._insert_coverage() - def add_variant_genes(self, variant_indexes:list, genes_to_add:list, ref_genes:dict): + def _add_variant_genes(self, variant_indexes: list, + genes_to_add: list, + ref_genes: dict): + """ + Add genes associated with the provided variants. + + Args: + variant_indexes (list): dbids of the variants + genes_to_add (list): the genes for each variant (str) + ref_genes (dict): genename: dbid + """ batch = [] for i in range(len(variant_indexes)): - connected_genes = [{'variant':variant_indexes[i], 'gene':ref_genes[gene]} for gene in genes_to_add[i] if gene] + connected_genes = [{'variant': variant_indexes[i], 'gene': ref_genes[gene]} + for gene in genes_to_add[i] + if gene] batch += connected_genes if not self.settings.dry_run: db.VariantGenes.insert_many(batch).execute() - def add_variant_transcripts(self, variant_indexes:list, transcripts_to_add:list, ref_transcripts:dict): + def _add_variant_transcripts(self, variant_indexes: list, + transcripts_to_add: list, + ref_transcripts: dict): + """ + Add transcripts associated with the provided variants. + + Args: + variant_indexes (list): dbids of the variants + transcripts_to_add (list): the transcripts for each variant (str) + ref_transcripts (dict): genename: dbid + """ batch = [] for i in range(len(variant_indexes)): - connected_transcripts = [{'variant':variant_indexes[i], 'transcript':ref_transcripts[transcript]} + connected_transcripts = [{'variant': variant_indexes[i], + 'transcript': ref_transcripts[transcript]} for transcript in transcripts_to_add[i]] batch += connected_transcripts if not self.settings.dry_run: db.VariantTranscripts.insert_many(batch).execute() - def log_insertion(self, counter, type, start): + @staticmethod + def _is_non_chromosome(chrom): + """ + Check if this is a GL or MT. + + GL is an unplaced scaffold, MT is mitochondria. + """ + return chrom.startswith('GL') or chrom.startswith('MT') + + def _log_insertion(self, counter, insertion_type, start): + """Log the progress of the import.""" action = "Inserted" if not self.settings.dry_run else "Dry-ran insertion of" - logging.info("{} {} {} records in {}".format(action, counter, type, self._time_since(start))) + logging.info("{} {} {} records in {}".format(action, + counter, + insertion_type, + self._time_since(start))) + + def _parse_baseinfo(self, header, line): + """ + Parse the fixed columns of a vcf data line. + + Args: + header (list): tuples of titles and converter functions for the colums of interest. + Ex ["chrom", str), ("pos", int)]. + line (str): a vcf line + + Returns: + dict: the parsed info as specified by the header, plus the dataset_version. + + """ + base = {'dataset_version': self.dataset_version} + line_info = line.split("\t") + for i, (title, conv) in enumerate(header): + base[title] = conv(line_info[i]) + return base + + def _parse_bnd_alleles(self, base, info): + """Parse alleles of a structural variant (BND) in a manta file.""" + batch = [] + for alt in base['alt'].split(","): + data = dict(base) + data['allele_freq'] = float(info.get('FRQ')) + data['alt'], data['mate_chrom'], data['mate_start'] = \ + re.search(r'(.+)[[\]](.*?):(\d+)[[\]]', alt).groups() + if self._is_non_chromosome(data['mate_chrom']): + # A BND from a chromosome to a non-chromosome. + # TODO ask a bioinformatician if these cases should be included or not # pylint: disable=fixme + continue + data['mate_id'] = info.get('MATEID', '') + data['variant_id'] = '{}-{}-{}-{}'.format(data['chrom'], + data['pos'], + data['ref'], + alt) + # Note: these two fields are not present in our data, will always default to 0. + # Set to 0 rather than None, as the type should be int (according to the Beacon + # API specificition). + data['allele_count'] = info.get('AC', 0) + data['allele_num'] = info.get('AN', 0) + + batch += [data] + if self.settings.add_reversed_mates: + # If the vcf only contains one line per breakend, + # add the reversed version to the database here. + reversed_mates = dict(data) + # Note: in general, ref and alt cannot be assumed to be the same in the + # reversed direction, but our data (so far) only contains N, so we just + # keep them as is for now. + reversed_mates.update({'mate_chrom': data['chrom'], + 'chrom': data['mate_chrom'], + 'mate_start': data['pos'], + 'pos': data['mate_start'], + 'chrom_id': data['mate_id'], + 'mate_id': data['chrom_id']}) + reversed_mates['variant_id'] = '{}-{}-{}-{}'.format(reversed_mates['chrom'], + reversed_mates['pos'], + reversed_mates['ref'], + alt) + batch += [reversed_mates] + + return batch + + @staticmethod + def _parse_info(line): + """Parse the INFO field of a vcf line.""" + parts = re.split(r';(?=\w)', line.split('\t')[7]) + return {x[0]: x[1] for x in map(lambda s: s.split('=', 1) if '=' in s else (s, s), parts)} diff --git a/scripts/importer/data_importer/reference_set_importer.py b/scripts/importer/data_importer/reference_set_importer.py index 66a9bed1f..1f7e6f342 100644 --- a/scripts/importer/data_importer/reference_set_importer.py +++ b/scripts/importer/data_importer/reference_set_importer.py @@ -1,4 +1,5 @@ #!/usr/bin/env python3 +"""Import a reference set into db.""" import os import re @@ -7,16 +8,20 @@ import shutil import logging import zipfile -from peewee import IntegrityError, fn +from peewee import fn import db from .data_importer import DataImporter -class ReferenceSetImporter(DataImporter): - GENCODE = "ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_human/release_{a.gencode_version}/gencode.v{a.gencode_version}.annotation.gtf.gz" +class ReferenceSetImporter(DataImporter): # pylint: disable=too-many-instance-attributes + """Import a reference set into db.""" + + GENCODE = ("ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_human/" + + "release_{a.gencode_version}/gencode.v{a.gencode_version}.annotation.gtf.gz") DBNSFP = "ftp://dbnsfp:dbnsfp@dbnsfp.softgenetics.com/dbNSFPv{a.dbnsfp_version}.zip" ENSEMBL = ("ensembldb.ensembl.org", "anonymous", "") def __init__(self, settings): + """Set the provided settings and prepare variables.""" super().__init__(settings) # counters for statistics and progress @@ -27,7 +32,7 @@ def __init__(self, settings): 'transcripts': 0, 'features': 0} - # dictionaries to hold data while processing + # lists to hold data while processing self.genes = [] self.transcripts = [] self.features = [] @@ -37,13 +42,25 @@ def __init__(self, settings): self.dbnsfp = None self.ensembl = None + # database ids for genes, transcripts + self.gene_db_ids = {} + self.transcript_db_ids = {} + + self.db_reference = db.ReferenceSet(name=self.settings.ref_name, + reference_build=self.settings.assembly_id, + ensembl_version=self.settings.ensembl_version, + gencode_version=self.settings.gencode_version, + dbnsfp_version=self.settings.dbnsfp_version) + def _insert_features(self): + """Insert gene features (e.g. intron) into db.""" logging.info("Inserting features into database") start = time.time() last_progress = -1 batch = [] + i = 0 with db.database.atomic(): - for i, feature in enumerate(self.features): + for feature in self.features: batch += [{'gene':self.gene_db_ids[feature['gene_id']], 'transcript':self.transcript_db_ids[feature['transcript_id']], 'chrom':feature['chrom'], @@ -58,19 +75,24 @@ def _insert_features(self): batch = [] last_progress = self._update_progress_bar(i, len(self.features), last_progress) + i += 1 + if batch: if not self.settings.dry_run: db.Feature.insert_many(batch).execute() - last_progress = self._update_progress_bar(i, len(self.features), last_progress, finished=True) + + last_progress = self._update_progress_bar(i, len(self.features), + last_progress, finished=True) logging.info("Features inserted in {}".format(self._time_since(start))) def _insert_genes(self): + """Insert gene intformation into db.""" logging.info("Inserting genes into database") start = time.time() - self.gene_db_ids = {} last_progress = -1 - for i, gene in enumerate(self.genes): + i = 0 + for gene in self.genes: # As far as I know I can't batch insert these and still get the id's back db_gene = db.Gene(reference_set=self.db_reference, gene_id=gene['gene_id'], @@ -96,17 +118,15 @@ def _insert_genes(self): pass last_progress = self._update_progress_bar(i, len(self.genes), last_progress) + i += 1 + last_progress = self._update_progress_bar(i, len(self.genes), last_progress, finished=True) - logging.info("Genes inserted in {}".format(self._time_since(start))) + logging.info(f"Genes inserted in {self._time_since(start)}") def _insert_reference(self): + """Insert information (header) about the references into db.""" logging.info("inserting reference header") - self.db_reference = db.ReferenceSet(name=self.settings.ref_name, - reference_build=self.settings.assembly_id, - ensembl_version=self.settings.ensembl_version, - gencode_version=self.settings.gencode_version, - dbnsfp_version=self.settings.dbnsfp_version) if self.settings.dry_run: max_id = db.ReferenceSet.select(fn.Max(db.ReferenceSet.id)).get() @@ -116,38 +136,42 @@ def _insert_reference(self): self.db_reference.id = max_id.id + 1 else: self.db_reference.save() - logging.info("Reference %s created", self.db_reference.id) + logging.info(f"Reference {self.db_reference.id} created") def _insert_transcripts(self): + """Insert trabscripts into db.""" logging.info("Inserting transcripts into database") start = time.time() - self.transcript_db_ids = {} last_progress = -1 - for i, transcript in enumerate(self.transcripts): - db_transcript = db.Transcript(transcript_id=transcript['transcript_id'], - gene=self.gene_db_ids[transcript['gene_id']], - mim_annotation=transcript.get('mim_annotation', None), - mim_gene_accession=transcript.get('mim_gene_accession', None), - chrom=transcript['chrom'], - start=transcript['start'], - stop=transcript['stop'], - strand=transcript['strand']) + i = 0 + for transcript in self.transcripts: + db_trans = db.Transcript(transcript_id=transcript['transcript_id'], + gene=self.gene_db_ids[transcript['gene_id']], + mim_annotation=transcript.get('mim_annotation', None), + mim_gene_accession=transcript.get('mim_gene_accession', None), + chrom=transcript['chrom'], + start=transcript['start'], + stop=transcript['stop'], + strand=transcript['strand']) if self.settings.dry_run: self.transcript_db_ids[transcript['transcript_id']] = 0 else: - db_transcript.save() - self.transcript_db_ids[transcript['transcript_id']] = db_transcript.id + db_trans.save() + self.transcript_db_ids[transcript['transcript_id']] = db_trans.id last_progress = self._update_progress_bar(i, len(self.transcripts), last_progress) - last_progress = self._update_progress_bar(i, len(self.transcripts), last_progress, finished=True) + i += 1 + + last_progress = self._update_progress_bar(i, len(self.transcripts), + last_progress, finished=True) logging.info("Transcripts inserted in {}".format(self._time_since(start))) def _open_dbnsfp(self): """ - Downloads (if needed) and opens the given dbNSFP file. + Download (if needed) and open the given dbNSFP file. Only a small part, 'dbNSFP2.9_gene' of the ~13Gb file is needed, but in order to get it we have to download the entire file, extract the part @@ -156,7 +180,7 @@ def _open_dbnsfp(self): logging.info("----- Opening dbNSFP file -----") url = ReferenceSetImporter.DBNSFP.format(a=self.settings) filename = url.split("/")[-1] - match = re.match("^\d+.\d+", self.settings.dbnsfp_version) + match = re.match(r"^\d+.\d+", self.settings.dbnsfp_version) if match: dbnsfp_gene_version = match.group(0) else: @@ -186,16 +210,13 @@ def _open_dbnsfp(self): self.dbnsfp = self._open(dbnsfp_gzip) def _open_ensembl(self): - """ - Connects to the given ensembl database. - """ + """Connect to the given ensembl database.""" logging.info("----- Opening ensembl database connection -----") - self.ensembl = self._connect(*(ReferenceSetImporter.ENSEMBL + (self.settings.ensembl_version,))) + self.ensembl = self._connect(*(ReferenceSetImporter.ENSEMBL + + (self.settings.ensembl_version,))) def _open_gencode(self): - """ - Downloads (if needed) and opens the given gencode file - """ + """Download (if needed) and opens the given gencode file.""" logging.info("----- Opening gencode file -----") url = ReferenceSetImporter.GENCODE.format(a=self.settings) filename = url.split("/")[-1] @@ -206,6 +227,7 @@ def _open_gencode(self): self.gencode = self._download_and_open(url) def _read_dbnsfp(self): + """Read dbNSFP data.""" start = time.time() header = None logging.info("Adding dbNSFP annotation") @@ -237,9 +259,7 @@ def _read_dbnsfp(self): logging.info("dbNSFP information added in {}.".format(self._time_since(start))) def _read_ensembl(self): - """ - Reads the ensembl information into the gene dictionary - """ + """Read the ensembl information into the gene dictionary.""" query = """SELECT g.stable_id, t.stable_id FROM gene g @@ -255,18 +275,24 @@ def _read_ensembl(self): canonical_dict[transcript[0]] = transcript[1] last_progress = -1.0 - for i, gene in enumerate(self.genes): + i = 0 + for gene in self.genes: if gene['gene_id'] in canonical_dict: self.genes[i]['canonical_transcript'] = canonical_dict[gene['gene_id']] self.counters['genes'] += 1 - if self.numbers['genes'] != None: + if self.numbers['genes'] is not None: last_progress = self._update_progress_bar(i, self.numbers['genes'], last_progress) - if self.numbers['genes'] != None: - last_progress = self._update_progress_bar(i, self.numbers['genes'], last_progress, finished=True) - logging.info("Canonical transcript information from ensembl added in {}.".format(self._time_since(start))) + i += 1 + + if self.numbers['genes'] is not None: + last_progress = self._update_progress_bar(i, self.numbers['genes'], + last_progress, finished=True) + logging.info("Canonical transcript information from ensembl " + + f"added in {self._time_since(start)}.") def count_entries(self): + """Count the number of entries.""" logging.info("Counting features in gencode file (for progress bar)") start = time.time() self.numbers['genes'] = 0 @@ -292,18 +318,21 @@ def count_entries(self): self.gencode.rewind() - pad = max([len("{:,}".format(self.numbers[t])) for t in ["genes", "transcripts", "features"]]) + pad = max([len("{:,}".format(self.numbers[t])) + for t in ["genes", "transcripts", "features"]]) logging.info("Parsed file in {:3.1f}s".format(time.time()-start)) logging.info("Genes : {0:>{pad},}".format(self.numbers['genes'], pad=pad)) logging.info("Transcripts: {0:>{pad},}".format(self.numbers['transcripts'], pad=pad)) logging.info("Features : {0:>{pad},}".format(self.numbers['features'], pad=pad)) def prepare_data(self): + """Prepare for import of data.""" self._open_gencode() self._open_dbnsfp() self._open_ensembl() def start_import(self): + """Start the data import.""" start = time.time() logging.info("Reading gencode data into buffers.") last_progress = -1.0 @@ -328,7 +357,9 @@ def start_import(self): # only progress for genes to keep it simple if self.numbers['genes'] is not None: - last_progress = self._update_progress_bar(self.counters['genes'], self.numbers['genes'], last_progress) + last_progress = self._update_progress_bar(self.counters['genes'], + self.numbers['genes'], + last_progress) if values[2] == 'gene': data['name'] = info['gene_name'] self.genes += [data] @@ -347,11 +378,14 @@ def start_import(self): self.counters['features'] += 1 continue - except Exception as error: + except Exception as error: # pylint: disable=broad-except logging.error("{}".format(error)) break if self.numbers['genes'] is not None: - last_progress = self._update_progress_bar(self.counters['genes'], self.numbers['genes'], last_progress, finished=True) + last_progress = self._update_progress_bar(self.counters['genes'], + self.numbers['genes'], + last_progress, + finished=True) logging.info("Gencode data read into buffers in {}.".format(self._time_since(start))) self._read_ensembl() self._read_dbnsfp() @@ -360,9 +394,12 @@ def start_import(self): self._insert_transcripts() self._insert_features() - def add_other_names(self, gene_dbid:int, other_names:list): + def add_other_names(self, gene_dbid: int, other_names: list): + """Add alternative names for the gene.""" if not gene_dbid or not other_names: return - batch = [{'gene':gene_dbid, 'name':other_name} for other_name in other_names if other_name != '.' and other_name] + batch = [{'gene':gene_dbid, 'name':other_name} + for other_name in other_names + if other_name != '.' and other_name] if not self.settings.dry_run and batch: db.GeneOtherNames.insert_many(batch).execute() diff --git a/scripts/importer/importer.py b/scripts/importer/importer.py index e489efae6..435a3103d 100755 --- a/scripts/importer/importer.py +++ b/scripts/importer/importer.py @@ -12,7 +12,6 @@ """ from data_importer.reference_set_importer import ReferenceSetImporter -from data_importer.old_db_importer import OldDbImporter from data_importer.raw_data_importer import RawDataImporter if __name__ == '__main__': @@ -77,9 +76,6 @@ help="Insert new reference set.") PARSER.add_argument("--add_raw_data", action="store_true", help="Adds a Coverage and Variants to the database.") - PARSER.add_argument("--move_studies", action="store_true", - help=("Moves studies and datasets from an old database " - "to a new one.")) PARSER.add_argument("--dry_run", action="store_true", help="Do not insert anything into the database") @@ -101,7 +97,8 @@ PARSER.add_argument("--add_mates", action="store_true", help=("Parse MANTA file and add the breakends to the db")) PARSER.add_argument("--add_reversed_mates", action="store_true", - help=("Assume input data only contain one line per BND, covering both directions")) + help=("Assume input data only contain one line per BND, " + + "covering both directions")) ARGS = PARSER.parse_args() @@ -111,9 +108,9 @@ if ARGS.add_reference: logging.info("Adding a new reference set using these sources:") - logging.info(" - Gencode: %s", ARGS.gencode_version) - logging.info(" - Ensembl: %s", ARGS.ensembl_version) - logging.info(" - dbNSFP: %s", ARGS.dbnsfp_version) + logging.info(f" - Gencode: {ARGS.gencode_version}") + logging.info(f" - Ensembl: {ARGS.ensembl_version}") + logging.info(f" - dbNSFP: {ARGS.dbnsfp_version}") IMPORTER = ReferenceSetImporter(ARGS) IMPORTER.prepare_data() @@ -121,13 +118,8 @@ IMPORTER.count_entries() IMPORTER.start_import() - if ARGS.move_studies: - IMPORTER = OldDbImporter(ARGS) - IMPORTER.prepare_data() - IMPORTER.start_import() - if ARGS.add_raw_data: - logging.info("Adding raw data %s", "(dry run)" if ARGS.dry_run else '') + logging.info(f"Adding raw data {'(dry run)' if ARGS.dry_run else ''}") IMPORTER = RawDataImporter(ARGS) IMPORTER.prepare_data() if not ARGS.disable_progress: diff --git a/scripts/importer/requirements.txt b/scripts/importer/requirements.txt index 6bf362d48..be085d36e 100644 --- a/scripts/importer/requirements.txt +++ b/scripts/importer/requirements.txt @@ -1,3 +1,3 @@ -mysqlclient==1.3.13 -peewee==2.10.2 -psycopg2-binary==2.7.5 +mysqlclient==1.4.2.post1 +peewee==3.9.6 +psycopg2-binary==2.8.3 diff --git a/scripts/importer/tests/data/base_info.sql b/scripts/importer/tests/data/base_info.sql new file mode 100644 index 000000000..d049101b2 --- /dev/null +++ b/scripts/importer/tests/data/base_info.sql @@ -0,0 +1,35 @@ +SET statement_timeout = 0; +SET lock_timeout = 0; +SET idle_in_transaction_session_timeout = 0; +SET client_encoding = 'UTF8'; +SET standard_conforming_strings = on; +SELECT pg_catalog.set_config('search_path', '', false); +SET check_function_bodies = false; +SET client_min_messages = warning; +SET row_security = off; + +COPY data.collections (id, study_name, ethnicity) FROM stdin; +1 reg undefined +2 reg undefined +\. + +COPY data.studies (id, pi_name, pi_email, contact_name, contact_email, title, study_description, publication_date, ref_doi) FROM stdin; +1 name email name email SweGen \N 2001-01-01 00:00:00 doi +2 name2 email2 name2 email2 SweGen2 \N 2001-01-02 00:00:00 doi +\. + +COPY data.datasets (id, study, short_name, full_name, browser_uri, beacon_uri, beacon_description, avg_seq_depth, seq_type, seq_tech, seq_center, dataset_size) FROM stdin; +1 1 Dataset 1 Dataset 1 url \N \N 0 type method place 0 +2 2 Dataset 2 Dataset 2 url \N \N 0 type method place 0 +\. + +COPY data.dataset_versions (id, dataset, reference_set, dataset_version, dataset_description, terms, available_from, ref_doi, data_contact_name, data_contact_link, num_variants, coverage_levels, portal_avail, file_access, beacon_access) FROM stdin; +1 1 1 Version 1 desc terms 2001-01-01 00:00:00 doi place email \N {1,5,10,15,20,25,30,50,100} TRUE REGISTERED PUBLIC +2 1 1 Version 2 desc terms 2001-01-02 00:00:00 doi place email \N {1,5,10,15,20,25,30,50,100} TRUE REGISTERED PUBLIC +3 2 1 Version 1 desc terms 2001-01-02 00:00:00 doi place email \N {1,5,10,15,20,25,30,50,100} TRUE REGISTERED PUBLIC +\. + +COPY data.sample_sets (id, dataset, collection, sample_size, phenotype) FROM stdin; +1 1 1 0 Undefined +2 2 1 0 Undefined +\. diff --git a/scripts/importer/tests/data/dataset1_1.vcf b/scripts/importer/tests/data/dataset1_1.vcf new file mode 100644 index 000000000..eedf00c83 --- /dev/null +++ b/scripts/importer/tests/data/dataset1_1.vcf @@ -0,0 +1,156 @@ +##fileformat=VCFv4.1 +##FILTER= +##ALT= +##FILTER= +##FILTER= +##FILTER= +##FILTER= +##FILTER= +##FILTER= +##FILTER= +##FILTER= +##FILTER= +##FILTER= +##GVCFBlock=minGQ=0(inclusive),maxGQ=1(exclusive) +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##INFO= +##INFO= +##VEP="v95" time="2019-01-24 15:35:16" ensembl-funcgen=95.94439f4 ensembl-io=95.bd1a78d ensembl-variation=95.858de3e ensembl=95.4f83453 1000genomes="phase3" COSMIC="86" ClinVar="201810" ESP="20141103" HGMD-PUBLIC="20174" assembly="GRCh37.p13" dbSNP="151" gencode="GENCODE 19" genebuild="2011-04" gnomAD="170228" polyphen="2.2.2" refseq="01_2015" regbuild="1.0" sift="sift5.2.2" +##INFO= +##LoF=Loss-of-function annotation (HC = High Confidence; LC = Low Confidence) +##LoF_filter=Reason for LoF not being HC +##LoF_flags=Possible warning flags for LoF +##LoF_info=Info used for LoF annotation +##bcftools_normVersion=1.2+htslib-1.2.1 +##bcftools_normCommand=norm -m+any -Oz ACpop.vep.vcf.gz +22 18118637 22:30786 A G 212919 PASS AC=600;AF=1;AN=600;BaseQRankSum=1.45;ClippingRankSum=1.24;DP=7320;FS=0;GQ_MEAN=69.99;GQ_STDDEV=18.61;HW=0;InbreedingCoeff=-0;MLEAC=600;MLEAF=1;MQ=60;MQ0=0;MQRankSum=-0.413;NCC=0;QD=29.98;ReadPosRankSum=0.867;SOR=0.162;VQSLOD=3.22;culprit=FS;CSQ=G|upstream_gene_variant|MODIFIER|BCL2L13|ENSG00000099968|Transcript|ENST00000317582|protein_coding||||||||||rs4256048|1|2719|1||SNV|HGNC|17164|YES|||CCDS13746.1|ENSP00000318883|Q9BXK5|B2RB43|UPI000004F301||Ensembl|A|A||||||||1|1|1|1|1|1||||||||||||1|AFR&AMR&EAS&EUR&SAS||||||||||||,G|upstream_gene_variant|MODIFIER|BCL2L13|ENSG00000099968|Transcript|ENST00000337612|protein_coding||||||||||rs4256048|1|2893|1||SNV|HGNC|17164||||CCDS59448.1|ENSP00000338932|Q9BXK5||UPI00001A3E35||Ensembl|A|A||||||||1|1|1|1|1|1||||||||||||1|AFR&AMR&EAS&EUR&SAS||||||||||||,G|upstream_gene_variant|MODIFIER|BCL2L13|ENSG00000099968|Transcript|ENST00000355028|protein_coding||||||||||rs4256048|1|2940|1||SNV|HGNC|17164||||CCDS59447.1|ENSP00000347133||E9PDD6|UPI0000246DFE||Ensembl|A|A||||||||1|1|1|1|1|1||||||||||||1|AFR&AMR&EAS&EUR&SAS||||||||||||,G|intron_variant&non_coding_transcript_variant|MODIFIER|BCL2L13|ENSG00000099968|Transcript|ENST00000399781|processed_transcript||1/4|ENST00000399781.1:n.53-2231A>G|||||||rs4256048|1||1||SNV|HGNC|17164||||||||||Ensembl|A|A||||||||1|1|1|1|1|1||||||||||||1|AFR&AMR&EAS&EUR&SAS||||||||||||,G|intron_variant|MODIFIER|BCL2L13|ENSG00000099968|Transcript|ENST00000399782|protein_coding||1/6|ENST00000399782.1:c.-649-2231A>G|||||||rs4256048|1||1||SNV|HGNC|17164|||||ENSP00000382682|Q9BXK5||UPI000002A4BC||Ensembl|A|A||||||||1|1|1|1|1|1||||||||||||1|AFR&AMR&EAS&EUR&SAS||||||||||||,G|upstream_gene_variant|MODIFIER|BCL2L13|ENSG00000099968|Transcript|ENST00000464649|processed_transcript||||||||||rs4256048|1|2886|1||SNV|HGNC|17164||||||||||Ensembl|A|A||||||||1|1|1|1|1|1||||||||||||1|AFR&AMR&EAS&EUR&SAS||||||||||||,G|upstream_gene_variant|MODIFIER|BCL2L13|ENSG00000099968|Transcript|ENST00000493680|protein_coding||||||||||rs4256048|1|2901|1||SNV|HGNC|17164|||||ENSP00000434764|Q9BXK5||UPI000002A4BC||Ensembl|A|A||||||||1|1|1|1|1|1||||||||||||1|AFR&AMR&EAS&EUR&SAS||||||||||||,G|upstream_gene_variant|MODIFIER|BCL2L13|ENSG00000099968|Transcript|ENST00000498133|nonsense_mediated_decay||||||||||rs4256048|1|2870|1||SNV|HGNC|17164|||||ENSP00000436321||F2Z2C3|UPI000155D5B6||Ensembl|A|A||||||||1|1|1|1|1|1||||||||||||1|AFR&AMR&EAS&EUR&SAS||||||||||||,G|upstream_gene_variant|MODIFIER|BCL2L13|ENSG00000099968|Transcript|ENST00000538149|protein_coding||||||||||rs4256048|1|2886|1||SNV|HGNC|17164|||||ENSP00000441344||B7Z238|UPI0001914B19||Ensembl|A|A||||||||1|1|1|1|1|1||||||||||||1|AFR&AMR&EAS&EUR&SAS||||||||||||,G|upstream_gene_variant|MODIFIER|BCL2L13|ENSG00000099968|Transcript|ENST00000543133|protein_coding||||||||||rs4256048|1|2870|1||SNV|HGNC|17164||||CCDS59448.1|ENSP00000437667|Q9BXK5||UPI00001A3E35||Ensembl|A|A||||||||1|1|1|1|1|1||||||||||||1|AFR&AMR&EAS&EUR&SAS||||||||||||,G|upstream_gene_variant|MODIFIER|BCL2L13|23786|Transcript|NM_001270726.1|protein_coding||||||||||rs4256048|1|2713|1||SNV|EntrezGene|17164|||||NP_001257655.1|||||RefSeq|A|A||||||||1|1|1|1|1|1||||||||||||1|AFR&AMR&EAS&EUR&SAS||||||||||||,G|upstream_gene_variant|MODIFIER|BCL2L13|23786|Transcript|NM_001270727.1|protein_coding||||||||||rs4256048|1|2713|1||SNV|EntrezGene|17164|||||NP_001257656.1|||||RefSeq|A|A||||||||1|1|1|1|1|1||||||||||||1|AFR&AMR&EAS&EUR&SAS||||||||||||,G|upstream_gene_variant|MODIFIER|BCL2L13|23786|Transcript|NM_001270728.1|protein_coding||||||||||rs4256048|1|2713|1||SNV|EntrezGene|17164|||||NP_001257657.1|||||RefSeq|A|A||||||||1|1|1|1|1|1||||||||||||1|AFR&AMR&EAS&EUR&SAS||||||||||||,G|upstream_gene_variant|MODIFIER|BCL2L13|23786|Transcript|NM_001270729.1|protein_coding||||||||||rs4256048|1|2713|1||SNV|EntrezGene|17164|||||NP_001257658.1|||||RefSeq|A|A||||||||1|1|1|1|1|1||||||||||||1|AFR&AMR&EAS&EUR&SAS||||||||||||,G|upstream_gene_variant|MODIFIER|BCL2L13|23786|Transcript|NM_001270730.1|protein_coding||||||||||rs4256048|1|2713|1||SNV|EntrezGene|17164|||||NP_001257659.1|||||RefSeq|A|A||||||||1|1|1|1|1|1||||||||||||1|AFR&AMR&EAS&EUR&SAS||||||||||||,G|upstream_gene_variant|MODIFIER|BCL2L13|23786|Transcript|NM_001270731.1|protein_coding||||||||||rs4256048|1|2713|1||SNV|EntrezGene|17164|||||NP_001257660.1|||||RefSeq|A|A||||||||1|1|1|1|1|1||||||||||||1|AFR&AMR&EAS&EUR&SAS||||||||||||,G|upstream_gene_variant|MODIFIER|BCL2L13|23786|Transcript|NM_001270732.1|protein_coding||||||||||rs4256048|1|2713|1||SNV|EntrezGene|17164|||||NP_001257661.1|||||RefSeq|A|A||||||||1|1|1|1|1|1||||||||||||1|AFR&AMR&EAS&EUR&SAS||||||||||||,G|upstream_gene_variant|MODIFIER|BCL2L13|23786|Transcript|NM_001270734.1|protein_coding||||||||||rs4256048|1|2713|1||SNV|EntrezGene|17164|||||NP_001257663.1|||||RefSeq|A|A||||||||1|1|1|1|1|1||||||||||||1|AFR&AMR&EAS&EUR&SAS||||||||||||,G|upstream_gene_variant|MODIFIER|BCL2L13|23786|Transcript|NM_001270735.1|protein_coding||||||||||rs4256048|1|2713|1||SNV|EntrezGene|17164|||||NP_001257664.1|||||RefSeq|A|A||||||||1|1|1|1|1|1||||||||||||1|AFR&AMR&EAS&EUR&SAS||||||||||||,G|upstream_gene_variant|MODIFIER|BCL2L13|23786|Transcript|NM_015367.3|protein_coding||||||||||rs4256048|1|2713|1||SNV|EntrezGene|17164|||||NP_056182.2|||||RefSeq|A|A||||||||1|1|1|1|1|1||||||||||||1|AFR&AMR&EAS&EUR&SAS||||||||||||,G|intron_variant|MODIFIER|BCL2L13|23786|Transcript|XM_005261231.1|protein_coding||1/6|XM_005261231.1:c.-592-2231A>G|||||||rs4256048|1||1||SNV|EntrezGene|17164|YES||||XP_005261288.1|||||RefSeq|A|A||||||||1|1|1|1|1|1||||||||||||1|AFR&AMR&EAS&EUR&SAS||||||||||||,G|upstream_gene_variant|MODIFIER|BCL2L13|23786|Transcript|XM_005261232.1|protein_coding||||||||||rs4256048|1|2713|1||SNV|EntrezGene|17164|||||XP_005261289.1|||||RefSeq|A|A||||||||1|1|1|1|1|1||||||||||||1|AFR&AMR&EAS&EUR&SAS||||||||||||,G|intron_variant|MODIFIER|BCL2L13|23786|Transcript|XM_005261233.1|protein_coding||1/5|XM_005261233.1:c.-835-2231A>G|||||||rs4256048|1||1||SNV|EntrezGene|17164|||||XP_005261290.1|||||RefSeq|A|A||||||||1|1|1|1|1|1||||||||||||1|AFR&AMR&EAS&EUR&SAS|||||||||||| +22 18159071 22:31233 CA C 159520 PASS AC=526;AF=0.877;AN=600;BaseQRankSum=0.213;ClippingRankSum=-0.194;DP=7580;FS=0.967;GQ_MEAN=87.66;GQ_STDDEV=54.47;HW=10.9;InbreedingCoeff=-0.1107;MLEAC=527;MLEAF=0.878;MQ=60;MQ0=0;MQRankSum=0.024;NCC=0;POSITIVE_TRAIN_SITE;QD=23.78;ReadPosRankSum=0.588;SOR=0.707;VQSLOD=3.21;culprit=FS;CSQ=-|intron_variant|MODIFIER|BCL2L13|ENSG00000099968|Transcript|ENST00000317582|protein_coding||2/6|ENST00000317582.5:c.122-6900del|||||||rs11343596|1||1||deletion|HGNC|17164|YES|||CCDS13746.1|ENSP00000318883|Q9BXK5|B2RB43|UPI000004F301||Ensembl|A|A|||||||8|||||||||||||||||||||||||||||||,-|intron_variant|MODIFIER|BCL2L13|ENSG00000099968|Transcript|ENST00000337612|protein_coding||2/4|ENST00000337612.5:c.-138-6900del|||||||rs11343596|1||1||deletion|HGNC|17164||||CCDS59448.1|ENSP00000338932|Q9BXK5||UPI00001A3E35||Ensembl|A|A|||||||8|||||||||||||||||||||||||||||||,-|intron_variant|MODIFIER|BCL2L13|ENSG00000099968|Transcript|ENST00000355028|protein_coding||2/4|ENST00000355028.3:c.122-6900del|||||||rs11343596|1||1||deletion|HGNC|17164||||CCDS59447.1|ENSP00000347133||E9PDD6|UPI0000246DFE||Ensembl|A|A|||||||8|||||||||||||||||||||||||||||||,-|intron_variant&non_coding_transcript_variant|MODIFIER|BCL2L13|ENSG00000099968|Transcript|ENST00000399781|processed_transcript||3/4|ENST00000399781.1:n.823-6900del|||||||rs11343596|1||1||deletion|HGNC|17164||||||||||Ensembl|A|A|||||||8|||||||||||||||||||||||||||||||,-|intron_variant|MODIFIER|BCL2L13|ENSG00000099968|Transcript|ENST00000399782|protein_coding||3/6|ENST00000399782.1:c.122-6900del|||||||rs11343596|1||1||deletion|HGNC|17164|||||ENSP00000382682|Q9BXK5||UPI000002A4BC||Ensembl|A|A|||||||8|||||||||||||||||||||||||||||||,-|intron_variant|MODIFIER|BCL2L13|ENSG00000099968|Transcript|ENST00000418951|protein_coding||1/4|ENST00000418951.2:c.122-6900del|||||||rs11343596|1||1||deletion|HGNC|17164|||||ENSP00000410019||Q8IZP5|UPI00000740D0||Ensembl|A|A|||||||8|||||||||||||||||||||||||||||||,-|intron_variant&non_coding_transcript_variant|MODIFIER|BCL2L13|ENSG00000099968|Transcript|ENST00000464649|processed_transcript||1/3|ENST00000464649.1:n.131-6900del|||||||rs11343596|1||1||deletion|HGNC|17164||||||||||Ensembl|A|A|||||||8|||||||||||||||||||||||||||||||,-|intron_variant|MODIFIER|BCL2L13|ENSG00000099968|Transcript|ENST00000493680|protein_coding||2/5|ENST00000493680.1:c.122-6900del|||||||rs11343596|1||1||deletion|HGNC|17164|||||ENSP00000434764|Q9BXK5||UPI000002A4BC||Ensembl|A|A|||||||8|||||||||||||||||||||||||||||||,-|intron_variant&NMD_transcript_variant|MODIFIER|BCL2L13|ENSG00000099968|Transcript|ENST00000498133|nonsense_mediated_decay||2/5|ENST00000498133.1:c.122-6900del|||||||rs11343596|1||1||deletion|HGNC|17164|||||ENSP00000436321||F2Z2C3|UPI000155D5B6||Ensembl|A|A|||||||8|||||||||||||||||||||||||||||||,-|intron_variant|MODIFIER|BCL2L13|ENSG00000099968|Transcript|ENST00000538149|protein_coding||2/3|ENST00000538149.1:c.84+20482del|||||||rs11343596|1||1||deletion|HGNC|17164|||||ENSP00000441344||B7Z238|UPI0001914B19||Ensembl|A|A|||||||8|||||||||||||||||||||||||||||||,-|intron_variant|MODIFIER|BCL2L13|ENSG00000099968|Transcript|ENST00000543133|protein_coding||2/5|ENST00000543133.1:c.-208-6900del|||||||rs11343596|1||1||deletion|HGNC|17164||||CCDS59448.1|ENSP00000437667|Q9BXK5||UPI00001A3E35||Ensembl|A|A|||||||8|||||||||||||||||||||||||||||||,-|intron_variant|MODIFIER|BCL2L13|23786|Transcript|NM_001270726.1|protein_coding||1/5|NM_001270726.1:c.194-6900del|||||||rs11343596|1||1||deletion|EntrezGene|17164|||||NP_001257655.1|||||RefSeq|A|A|||||||8|||||||||||||||||||||||||||||||,-|intron_variant|MODIFIER|BCL2L13|23786|Transcript|NM_001270727.1|protein_coding||1/4|NM_001270727.1:c.194-6900del|||||||rs11343596|1||1||deletion|EntrezGene|17164|||||NP_001257656.1|||||RefSeq|A|A|||||||8|||||||||||||||||||||||||||||||,-|intron_variant|MODIFIER|BCL2L13|23786|Transcript|NM_001270728.1|protein_coding||2/3|NM_001270728.1:c.121+20482del|||||||rs11343596|1||1||deletion|EntrezGene|17164|||||NP_001257657.1|||||RefSeq|A|A|||||||8|||||||||||||||||||||||||||||||,-|intron_variant|MODIFIER|BCL2L13|23786|Transcript|NM_001270729.1|protein_coding||2/5|NM_001270729.1:c.-208-6900del|||||||rs11343596|1||1||deletion|EntrezGene|17164|||||NP_001257658.1|||||RefSeq|A|A|||||||8|||||||||||||||||||||||||||||||,-|intron_variant|MODIFIER|BCL2L13|23786|Transcript|NM_001270730.1|protein_coding||1/4|NM_001270730.1:c.-208-6900del|||||||rs11343596|1||1||deletion|EntrezGene|17164|||||NP_001257659.1|||||RefSeq|A|A|||||||8|||||||||||||||||||||||||||||||,-|intron_variant|MODIFIER|BCL2L13|23786|Transcript|NM_001270731.1|protein_coding||2/5|NM_001270731.1:c.-295-6900del|||||||rs11343596|1||1||deletion|EntrezGene|17164|||||NP_001257660.1|||||RefSeq|A|A|||||||8|||||||||||||||||||||||||||||||,-|intron_variant|MODIFIER|BCL2L13|23786|Transcript|NM_001270732.1|protein_coding||2/4|NM_001270732.1:c.122-6900del|||||||rs11343596|1||1||deletion|EntrezGene|17164|||||NP_001257661.1|||||RefSeq|A|A|||||||8|||||||||||||||||||||||||||||||,-|intron_variant|MODIFIER|BCL2L13|23786|Transcript|NM_001270734.1|protein_coding||2/4|NM_001270734.1:c.122-6900del|||||||rs11343596|1||1||deletion|EntrezGene|17164|||||NP_001257663.1|||||RefSeq|A|A|||||||8|||||||||||||||||||||||||||||||,-|intron_variant|MODIFIER|BCL2L13|23786|Transcript|NM_001270735.1|protein_coding||2/3|NM_001270735.1:c.122-6900del|||||||rs11343596|1||1||deletion|EntrezGene|17164|||||NP_001257664.1|||||RefSeq|A|A|||||||8|||||||||||||||||||||||||||||||,-|intron_variant|MODIFIER|BCL2L13|23786|Transcript|NM_015367.3|protein_coding||2/6|NM_015367.3:c.122-6900del|||||||rs11343596|1||1||deletion|EntrezGene|17164|||||NP_056182.2|||||RefSeq|A|A|||||||8|||||||||||||||||||||||||||||||,-|intron_variant&non_coding_transcript_variant|MODIFIER|BCL2L13|23786|Transcript|NR_073068.1|misc_RNA||2/4|NR_073068.1:n.287-6900del|||||||rs11343596|1||1||deletion|EntrezGene|17164||||||||||RefSeq|A|A|||||||8|||||||||||||||||||||||||||||||,-|intron_variant&non_coding_transcript_variant|MODIFIER|BCL2L13|23786|Transcript|NR_073069.1|misc_RNA||1/4|NR_073069.1:n.172-6900del|||||||rs11343596|1||1||deletion|EntrezGene|17164||||||||||RefSeq|A|A|||||||8|||||||||||||||||||||||||||||||,-|intron_variant|MODIFIER|BCL2L13|23786|Transcript|XM_005261231.1|protein_coding||2/6|XM_005261231.1:c.194-6900del|||||||rs11343596|1||1||deletion|EntrezGene|17164|YES||||XP_005261288.1|||||RefSeq|A|A|||||||8|||||||||||||||||||||||||||||||,-|intron_variant|MODIFIER|BCL2L13|23786|Transcript|XM_005261232.1|protein_coding||2/5|XM_005261232.1:c.122-6900del|||||||rs11343596|1||1||deletion|EntrezGene|17164|||||XP_005261289.1|||||RefSeq|A|A|||||||8|||||||||||||||||||||||||||||||,-|intron_variant|MODIFIER|BCL2L13|23786|Transcript|XM_005261233.1|protein_coding||3/5|XM_005261233.1:c.122-6900del|||||||rs11343596|1||1||deletion|EntrezGene|17164|||||XP_005261290.1|||||RefSeq|A|A|||||||8||||||||||||||||||||||||||||||| +22 18159407 22:31235 T C 253125 PASS AC=524;AF=0.873;AN=600;BaseQRankSum=-2.616;ClippingRankSum=-0.155;DP=10409;FS=0;GQ_MEAN=164.99;GQ_STDDEV=123.97;HW=12;InbreedingCoeff=-0.1149;MLEAC=524;MLEAF=0.873;MQ=60;MQ0=0;MQRankSum=-0.121;NCC=0;POSITIVE_TRAIN_SITE;QD=24.69;ReadPosRankSum=0.347;SOR=0.713;VQSLOD=6.91;culprit=FS;CSQ=C|intron_variant|MODIFIER|BCL2L13|ENSG00000099968|Transcript|ENST00000317582|protein_coding||2/6|ENST00000317582.5:c.122-6573T>C|||||||rs2535694|1||1||SNV|HGNC|17164|YES|||CCDS13746.1|ENSP00000318883|Q9BXK5|B2RB43|UPI000004F301||Ensembl|T|T||||||||0.8646|0.9281|0.853|0.9375|0.8151|0.7628||||||||||||0.9375|EAS||||||||||||,C|intron_variant|MODIFIER|BCL2L13|ENSG00000099968|Transcript|ENST00000337612|protein_coding||2/4|ENST00000337612.5:c.-138-6573T>C|||||||rs2535694|1||1||SNV|HGNC|17164||||CCDS59448.1|ENSP00000338932|Q9BXK5||UPI00001A3E35||Ensembl|T|T||||||||0.8646|0.9281|0.853|0.9375|0.8151|0.7628||||||||||||0.9375|EAS||||||||||||,C|intron_variant|MODIFIER|BCL2L13|ENSG00000099968|Transcript|ENST00000355028|protein_coding||2/4|ENST00000355028.3:c.122-6573T>C|||||||rs2535694|1||1||SNV|HGNC|17164||||CCDS59447.1|ENSP00000347133||E9PDD6|UPI0000246DFE||Ensembl|T|T||||||||0.8646|0.9281|0.853|0.9375|0.8151|0.7628||||||||||||0.9375|EAS||||||||||||,C|intron_variant&non_coding_transcript_variant|MODIFIER|BCL2L13|ENSG00000099968|Transcript|ENST00000399781|processed_transcript||3/4|ENST00000399781.1:n.823-6573T>C|||||||rs2535694|1||1||SNV|HGNC|17164||||||||||Ensembl|T|T||||||||0.8646|0.9281|0.853|0.9375|0.8151|0.7628||||||||||||0.9375|EAS||||||||||||,C|intron_variant|MODIFIER|BCL2L13|ENSG00000099968|Transcript|ENST00000399782|protein_coding||3/6|ENST00000399782.1:c.122-6573T>C|||||||rs2535694|1||1||SNV|HGNC|17164|||||ENSP00000382682|Q9BXK5||UPI000002A4BC||Ensembl|T|T||||||||0.8646|0.9281|0.853|0.9375|0.8151|0.7628||||||||||||0.9375|EAS||||||||||||,C|intron_variant|MODIFIER|BCL2L13|ENSG00000099968|Transcript|ENST00000418951|protein_coding||1/4|ENST00000418951.2:c.122-6573T>C|||||||rs2535694|1||1||SNV|HGNC|17164|||||ENSP00000410019||Q8IZP5|UPI00000740D0||Ensembl|T|T||||||||0.8646|0.9281|0.853|0.9375|0.8151|0.7628||||||||||||0.9375|EAS||||||||||||,C|intron_variant&non_coding_transcript_variant|MODIFIER|BCL2L13|ENSG00000099968|Transcript|ENST00000464649|processed_transcript||1/3|ENST00000464649.1:n.131-6573T>C|||||||rs2535694|1||1||SNV|HGNC|17164||||||||||Ensembl|T|T||||||||0.8646|0.9281|0.853|0.9375|0.8151|0.7628||||||||||||0.9375|EAS||||||||||||,C|intron_variant|MODIFIER|BCL2L13|ENSG00000099968|Transcript|ENST00000493680|protein_coding||2/5|ENST00000493680.1:c.122-6573T>C|||||||rs2535694|1||1||SNV|HGNC|17164|||||ENSP00000434764|Q9BXK5||UPI000002A4BC||Ensembl|T|T||||||||0.8646|0.9281|0.853|0.9375|0.8151|0.7628||||||||||||0.9375|EAS||||||||||||,C|intron_variant&NMD_transcript_variant|MODIFIER|BCL2L13|ENSG00000099968|Transcript|ENST00000498133|nonsense_mediated_decay||2/5|ENST00000498133.1:c.122-6573T>C|||||||rs2535694|1||1||SNV|HGNC|17164|||||ENSP00000436321||F2Z2C3|UPI000155D5B6||Ensembl|T|T||||||||0.8646|0.9281|0.853|0.9375|0.8151|0.7628||||||||||||0.9375|EAS||||||||||||,C|intron_variant|MODIFIER|BCL2L13|ENSG00000099968|Transcript|ENST00000538149|protein_coding||2/3|ENST00000538149.1:c.84+20809T>C|||||||rs2535694|1||1||SNV|HGNC|17164|||||ENSP00000441344||B7Z238|UPI0001914B19||Ensembl|T|T||||||||0.8646|0.9281|0.853|0.9375|0.8151|0.7628||||||||||||0.9375|EAS||||||||||||,C|intron_variant|MODIFIER|BCL2L13|ENSG00000099968|Transcript|ENST00000543133|protein_coding||2/5|ENST00000543133.1:c.-208-6573T>C|||||||rs2535694|1||1||SNV|HGNC|17164||||CCDS59448.1|ENSP00000437667|Q9BXK5||UPI00001A3E35||Ensembl|T|T||||||||0.8646|0.9281|0.853|0.9375|0.8151|0.7628||||||||||||0.9375|EAS||||||||||||,C|intron_variant|MODIFIER|BCL2L13|23786|Transcript|NM_001270726.1|protein_coding||1/5|NM_001270726.1:c.194-6573T>C|||||||rs2535694|1||1||SNV|EntrezGene|17164|||||NP_001257655.1|||||RefSeq|T|T||||||||0.8646|0.9281|0.853|0.9375|0.8151|0.7628||||||||||||0.9375|EAS||||||||||||,C|intron_variant|MODIFIER|BCL2L13|23786|Transcript|NM_001270727.1|protein_coding||1/4|NM_001270727.1:c.194-6573T>C|||||||rs2535694|1||1||SNV|EntrezGene|17164|||||NP_001257656.1|||||RefSeq|T|T||||||||0.8646|0.9281|0.853|0.9375|0.8151|0.7628||||||||||||0.9375|EAS||||||||||||,C|intron_variant|MODIFIER|BCL2L13|23786|Transcript|NM_001270728.1|protein_coding||2/3|NM_001270728.1:c.121+20809T>C|||||||rs2535694|1||1||SNV|EntrezGene|17164|||||NP_001257657.1|||||RefSeq|T|T||||||||0.8646|0.9281|0.853|0.9375|0.8151|0.7628||||||||||||0.9375|EAS||||||||||||,C|intron_variant|MODIFIER|BCL2L13|23786|Transcript|NM_001270729.1|protein_coding||2/5|NM_001270729.1:c.-208-6573T>C|||||||rs2535694|1||1||SNV|EntrezGene|17164|||||NP_001257658.1|||||RefSeq|T|T||||||||0.8646|0.9281|0.853|0.9375|0.8151|0.7628||||||||||||0.9375|EAS||||||||||||,C|intron_variant|MODIFIER|BCL2L13|23786|Transcript|NM_001270730.1|protein_coding||1/4|NM_001270730.1:c.-208-6573T>C|||||||rs2535694|1||1||SNV|EntrezGene|17164|||||NP_001257659.1|||||RefSeq|T|T||||||||0.8646|0.9281|0.853|0.9375|0.8151|0.7628||||||||||||0.9375|EAS||||||||||||,C|intron_variant|MODIFIER|BCL2L13|23786|Transcript|NM_001270731.1|protein_coding||2/5|NM_001270731.1:c.-295-6573T>C|||||||rs2535694|1||1||SNV|EntrezGene|17164|||||NP_001257660.1|||||RefSeq|T|T||||||||0.8646|0.9281|0.853|0.9375|0.8151|0.7628||||||||||||0.9375|EAS||||||||||||,C|intron_variant|MODIFIER|BCL2L13|23786|Transcript|NM_001270732.1|protein_coding||2/4|NM_001270732.1:c.122-6573T>C|||||||rs2535694|1||1||SNV|EntrezGene|17164|||||NP_001257661.1|||||RefSeq|T|T||||||||0.8646|0.9281|0.853|0.9375|0.8151|0.7628||||||||||||0.9375|EAS||||||||||||,C|intron_variant|MODIFIER|BCL2L13|23786|Transcript|NM_001270734.1|protein_coding||2/4|NM_001270734.1:c.122-6573T>C|||||||rs2535694|1||1||SNV|EntrezGene|17164|||||NP_001257663.1|||||RefSeq|T|T||||||||0.8646|0.9281|0.853|0.9375|0.8151|0.7628||||||||||||0.9375|EAS||||||||||||,C|intron_variant|MODIFIER|BCL2L13|23786|Transcript|NM_001270735.1|protein_coding||2/3|NM_001270735.1:c.122-6573T>C|||||||rs2535694|1||1||SNV|EntrezGene|17164|||||NP_001257664.1|||||RefSeq|T|T||||||||0.8646|0.9281|0.853|0.9375|0.8151|0.7628||||||||||||0.9375|EAS||||||||||||,C|intron_variant|MODIFIER|BCL2L13|23786|Transcript|NM_015367.3|protein_coding||2/6|NM_015367.3:c.122-6573T>C|||||||rs2535694|1||1||SNV|EntrezGene|17164|||||NP_056182.2|||||RefSeq|T|T||||||||0.8646|0.9281|0.853|0.9375|0.8151|0.7628||||||||||||0.9375|EAS||||||||||||,C|intron_variant&non_coding_transcript_variant|MODIFIER|BCL2L13|23786|Transcript|NR_073068.1|misc_RNA||2/4|NR_073068.1:n.287-6573T>C|||||||rs2535694|1||1||SNV|EntrezGene|17164||||||||||RefSeq|T|T||||||||0.8646|0.9281|0.853|0.9375|0.8151|0.7628||||||||||||0.9375|EAS||||||||||||,C|intron_variant&non_coding_transcript_variant|MODIFIER|BCL2L13|23786|Transcript|NR_073069.1|misc_RNA||1/4|NR_073069.1:n.172-6573T>C|||||||rs2535694|1||1||SNV|EntrezGene|17164||||||||||RefSeq|T|T||||||||0.8646|0.9281|0.853|0.9375|0.8151|0.7628||||||||||||0.9375|EAS||||||||||||,C|intron_variant|MODIFIER|BCL2L13|23786|Transcript|XM_005261231.1|protein_coding||2/6|XM_005261231.1:c.194-6573T>C|||||||rs2535694|1||1||SNV|EntrezGene|17164|YES||||XP_005261288.1|||||RefSeq|T|T||||||||0.8646|0.9281|0.853|0.9375|0.8151|0.7628||||||||||||0.9375|EAS||||||||||||,C|intron_variant|MODIFIER|BCL2L13|23786|Transcript|XM_005261232.1|protein_coding||2/5|XM_005261232.1:c.122-6573T>C|||||||rs2535694|1||1||SNV|EntrezGene|17164|||||XP_005261289.1|||||RefSeq|T|T||||||||0.8646|0.9281|0.853|0.9375|0.8151|0.7628||||||||||||0.9375|EAS||||||||||||,C|intron_variant|MODIFIER|BCL2L13|23786|Transcript|XM_005261233.1|protein_coding||3/5|XM_005261233.1:c.122-6573T>C|||||||rs2535694|1||1||SNV|EntrezGene|17164|||||XP_005261290.1|||||RefSeq|T|T||||||||0.8646|0.9281|0.853|0.9375|0.8151|0.7628||||||||||||0.9375|EAS|||||||||||| +22 18163136 22:31270 A C 167770 PASS AC=519;AF=0.868;AN=598;BaseQRankSum=0.67;ClippingRankSum=-0.34;DP=6358;FS=1.964;GQ_MEAN=88.4;GQ_STDDEV=77.33;HW=1.1;InbreedingCoeff=-0.0744;MLEAC=522;MLEAF=0.873;MQ=59.45;MQ0=0;MQRankSum=0.102;NCC=1;NEGATIVE_TRAIN_SITE;POSITIVE_TRAIN_SITE;QD=29.62;ReadPosRankSum=0.274;SOR=0.53;VQSLOD=0.808;culprit=FS;CSQ=C|intron_variant|MODIFIER|BCL2L13|ENSG00000099968|Transcript|ENST00000317582|protein_coding||2/6|ENST00000317582.5:c.122-2844A>C|||||||rs9605381|1||1||SNV|HGNC|17164|YES|||CCDS13746.1|ENSP00000318883|Q9BXK5|B2RB43|UPI000004F301||Ensembl|A|A||||||||0.8524|0.885|0.8473|0.9375|0.8151|0.7628||||||||||||0.9375|EAS||||||||||||,C|intron_variant|MODIFIER|BCL2L13|ENSG00000099968|Transcript|ENST00000337612|protein_coding||2/4|ENST00000337612.5:c.-138-2844A>C|||||||rs9605381|1||1||SNV|HGNC|17164||||CCDS59448.1|ENSP00000338932|Q9BXK5||UPI00001A3E35||Ensembl|A|A||||||||0.8524|0.885|0.8473|0.9375|0.8151|0.7628||||||||||||0.9375|EAS||||||||||||,C|intron_variant|MODIFIER|BCL2L13|ENSG00000099968|Transcript|ENST00000355028|protein_coding||2/4|ENST00000355028.3:c.122-2844A>C|||||||rs9605381|1||1||SNV|HGNC|17164||||CCDS59447.1|ENSP00000347133||E9PDD6|UPI0000246DFE||Ensembl|A|A||||||||0.8524|0.885|0.8473|0.9375|0.8151|0.7628||||||||||||0.9375|EAS||||||||||||,C|intron_variant&non_coding_transcript_variant|MODIFIER|BCL2L13|ENSG00000099968|Transcript|ENST00000399781|processed_transcript||3/4|ENST00000399781.1:n.823-2844A>C|||||||rs9605381|1||1||SNV|HGNC|17164||||||||||Ensembl|A|A||||||||0.8524|0.885|0.8473|0.9375|0.8151|0.7628||||||||||||0.9375|EAS||||||||||||,C|intron_variant|MODIFIER|BCL2L13|ENSG00000099968|Transcript|ENST00000399782|protein_coding||3/6|ENST00000399782.1:c.122-2844A>C|||||||rs9605381|1||1||SNV|HGNC|17164|||||ENSP00000382682|Q9BXK5||UPI000002A4BC||Ensembl|A|A||||||||0.8524|0.885|0.8473|0.9375|0.8151|0.7628||||||||||||0.9375|EAS||||||||||||,C|intron_variant|MODIFIER|BCL2L13|ENSG00000099968|Transcript|ENST00000418951|protein_coding||1/4|ENST00000418951.2:c.122-2844A>C|||||||rs9605381|1||1||SNV|HGNC|17164|||||ENSP00000410019||Q8IZP5|UPI00000740D0||Ensembl|A|A||||||||0.8524|0.885|0.8473|0.9375|0.8151|0.7628||||||||||||0.9375|EAS||||||||||||,C|intron_variant&non_coding_transcript_variant|MODIFIER|BCL2L13|ENSG00000099968|Transcript|ENST00000464649|processed_transcript||1/3|ENST00000464649.1:n.131-2844A>C|||||||rs9605381|1||1||SNV|HGNC|17164||||||||||Ensembl|A|A||||||||0.8524|0.885|0.8473|0.9375|0.8151|0.7628||||||||||||0.9375|EAS||||||||||||,C|intron_variant|MODIFIER|BCL2L13|ENSG00000099968|Transcript|ENST00000493680|protein_coding||2/5|ENST00000493680.1:c.122-2844A>C|||||||rs9605381|1||1||SNV|HGNC|17164|||||ENSP00000434764|Q9BXK5||UPI000002A4BC||Ensembl|A|A||||||||0.8524|0.885|0.8473|0.9375|0.8151|0.7628||||||||||||0.9375|EAS||||||||||||,C|intron_variant&NMD_transcript_variant|MODIFIER|BCL2L13|ENSG00000099968|Transcript|ENST00000498133|nonsense_mediated_decay||2/5|ENST00000498133.1:c.122-2844A>C|||||||rs9605381|1||1||SNV|HGNC|17164|||||ENSP00000436321||F2Z2C3|UPI000155D5B6||Ensembl|A|A||||||||0.8524|0.885|0.8473|0.9375|0.8151|0.7628||||||||||||0.9375|EAS||||||||||||,C|intron_variant|MODIFIER|BCL2L13|ENSG00000099968|Transcript|ENST00000538149|protein_coding||2/3|ENST00000538149.1:c.85-21873A>C|||||||rs9605381|1||1||SNV|HGNC|17164|||||ENSP00000441344||B7Z238|UPI0001914B19||Ensembl|A|A||||||||0.8524|0.885|0.8473|0.9375|0.8151|0.7628||||||||||||0.9375|EAS||||||||||||,C|intron_variant|MODIFIER|BCL2L13|ENSG00000099968|Transcript|ENST00000543133|protein_coding||2/5|ENST00000543133.1:c.-208-2844A>C|||||||rs9605381|1||1||SNV|HGNC|17164||||CCDS59448.1|ENSP00000437667|Q9BXK5||UPI00001A3E35||Ensembl|A|A||||||||0.8524|0.885|0.8473|0.9375|0.8151|0.7628||||||||||||0.9375|EAS||||||||||||,C|intron_variant|MODIFIER|BCL2L13|23786|Transcript|NM_001270726.1|protein_coding||1/5|NM_001270726.1:c.194-2844A>C|||||||rs9605381|1||1||SNV|EntrezGene|17164|||||NP_001257655.1|||||RefSeq|A|A||||||||0.8524|0.885|0.8473|0.9375|0.8151|0.7628||||||||||||0.9375|EAS||||||||||||,C|intron_variant|MODIFIER|BCL2L13|23786|Transcript|NM_001270727.1|protein_coding||1/4|NM_001270727.1:c.194-2844A>C|||||||rs9605381|1||1||SNV|EntrezGene|17164|||||NP_001257656.1|||||RefSeq|A|A||||||||0.8524|0.885|0.8473|0.9375|0.8151|0.7628||||||||||||0.9375|EAS||||||||||||,C|intron_variant|MODIFIER|BCL2L13|23786|Transcript|NM_001270728.1|protein_coding||2/3|NM_001270728.1:c.122-21873A>C|||||||rs9605381|1||1||SNV|EntrezGene|17164|||||NP_001257657.1|||||RefSeq|A|A||||||||0.8524|0.885|0.8473|0.9375|0.8151|0.7628||||||||||||0.9375|EAS||||||||||||,C|intron_variant|MODIFIER|BCL2L13|23786|Transcript|NM_001270729.1|protein_coding||2/5|NM_001270729.1:c.-208-2844A>C|||||||rs9605381|1||1||SNV|EntrezGene|17164|||||NP_001257658.1|||||RefSeq|A|A||||||||0.8524|0.885|0.8473|0.9375|0.8151|0.7628||||||||||||0.9375|EAS||||||||||||,C|intron_variant|MODIFIER|BCL2L13|23786|Transcript|NM_001270730.1|protein_coding||1/4|NM_001270730.1:c.-208-2844A>C|||||||rs9605381|1||1||SNV|EntrezGene|17164|||||NP_001257659.1|||||RefSeq|A|A||||||||0.8524|0.885|0.8473|0.9375|0.8151|0.7628||||||||||||0.9375|EAS||||||||||||,C|intron_variant|MODIFIER|BCL2L13|23786|Transcript|NM_001270731.1|protein_coding||2/5|NM_001270731.1:c.-295-2844A>C|||||||rs9605381|1||1||SNV|EntrezGene|17164|||||NP_001257660.1|||||RefSeq|A|A||||||||0.8524|0.885|0.8473|0.9375|0.8151|0.7628||||||||||||0.9375|EAS||||||||||||,C|intron_variant|MODIFIER|BCL2L13|23786|Transcript|NM_001270732.1|protein_coding||2/4|NM_001270732.1:c.122-2844A>C|||||||rs9605381|1||1||SNV|EntrezGene|17164|||||NP_001257661.1|||||RefSeq|A|A||||||||0.8524|0.885|0.8473|0.9375|0.8151|0.7628||||||||||||0.9375|EAS||||||||||||,C|intron_variant|MODIFIER|BCL2L13|23786|Transcript|NM_001270734.1|protein_coding||2/4|NM_001270734.1:c.122-2844A>C|||||||rs9605381|1||1||SNV|EntrezGene|17164|||||NP_001257663.1|||||RefSeq|A|A||||||||0.8524|0.885|0.8473|0.9375|0.8151|0.7628||||||||||||0.9375|EAS||||||||||||,C|intron_variant|MODIFIER|BCL2L13|23786|Transcript|NM_001270735.1|protein_coding||2/3|NM_001270735.1:c.122-2844A>C|||||||rs9605381|1||1||SNV|EntrezGene|17164|||||NP_001257664.1|||||RefSeq|A|A||||||||0.8524|0.885|0.8473|0.9375|0.8151|0.7628||||||||||||0.9375|EAS||||||||||||,C|intron_variant|MODIFIER|BCL2L13|23786|Transcript|NM_015367.3|protein_coding||2/6|NM_015367.3:c.122-2844A>C|||||||rs9605381|1||1||SNV|EntrezGene|17164|||||NP_056182.2|||||RefSeq|A|A||||||||0.8524|0.885|0.8473|0.9375|0.8151|0.7628||||||||||||0.9375|EAS||||||||||||,C|intron_variant&non_coding_transcript_variant|MODIFIER|BCL2L13|23786|Transcript|NR_073068.1|misc_RNA||2/4|NR_073068.1:n.287-2844A>C|||||||rs9605381|1||1||SNV|EntrezGene|17164||||||||||RefSeq|A|A||||||||0.8524|0.885|0.8473|0.9375|0.8151|0.7628||||||||||||0.9375|EAS||||||||||||,C|intron_variant&non_coding_transcript_variant|MODIFIER|BCL2L13|23786|Transcript|NR_073069.1|misc_RNA||1/4|NR_073069.1:n.172-2844A>C|||||||rs9605381|1||1||SNV|EntrezGene|17164||||||||||RefSeq|A|A||||||||0.8524|0.885|0.8473|0.9375|0.8151|0.7628||||||||||||0.9375|EAS||||||||||||,C|intron_variant|MODIFIER|BCL2L13|23786|Transcript|XM_005261231.1|protein_coding||2/6|XM_005261231.1:c.194-2844A>C|||||||rs9605381|1||1||SNV|EntrezGene|17164|YES||||XP_005261288.1|||||RefSeq|A|A||||||||0.8524|0.885|0.8473|0.9375|0.8151|0.7628||||||||||||0.9375|EAS||||||||||||,C|intron_variant|MODIFIER|BCL2L13|23786|Transcript|XM_005261232.1|protein_coding||2/5|XM_005261232.1:c.122-2844A>C|||||||rs9605381|1||1||SNV|EntrezGene|17164|||||XP_005261289.1|||||RefSeq|A|A||||||||0.8524|0.885|0.8473|0.9375|0.8151|0.7628||||||||||||0.9375|EAS||||||||||||,C|intron_variant|MODIFIER|BCL2L13|23786|Transcript|XM_005261233.1|protein_coding||3/5|XM_005261233.1:c.122-2844A>C|||||||rs9605381|1||1||SNV|EntrezGene|17164|||||XP_005261290.1|||||RefSeq|A|A||||||||0.8524|0.885|0.8473|0.9375|0.8151|0.7628||||||||||||0.9375|EAS|||||||||||| +22 18163308 22:31280 G A 49925.8 VQSRTrancheSNP99.70to99.90 AC=409;AF=0.746;AN=548;BaseQRankSum=0.573;ClippingRankSum=0.135;DP=3616;FS=3.907;GQ_MEAN=30.94;GQ_STDDEV=30.13;HW=137.2;InbreedingCoeff=0.256;MLEAC=455;MLEAF=0.83;MQ=58.52;MQ0=0;MQRankSum=0.289;NCC=26;NEGATIVE_TRAIN_SITE;QD=24.33;ReadPosRankSum=0.067;SOR=0.731;VQSLOD=-3.268;culprit=DP;CSQ=A|intron_variant|MODIFIER|BCL2L13|ENSG00000099968|Transcript|ENST00000317582|protein_coding||2/6|ENST00000317582.5:c.122-2672G>A|||||||rs3994810|1||1||SNV|HGNC|17164|YES|||CCDS13746.1|ENSP00000318883|Q9BXK5|B2RB43|UPI000004F301||Ensembl|G|G||||||||||||||||||||||||||||||||||||||,A|intron_variant|MODIFIER|BCL2L13|ENSG00000099968|Transcript|ENST00000337612|protein_coding||2/4|ENST00000337612.5:c.-138-2672G>A|||||||rs3994810|1||1||SNV|HGNC|17164||||CCDS59448.1|ENSP00000338932|Q9BXK5||UPI00001A3E35||Ensembl|G|G||||||||||||||||||||||||||||||||||||||,A|intron_variant|MODIFIER|BCL2L13|ENSG00000099968|Transcript|ENST00000355028|protein_coding||2/4|ENST00000355028.3:c.122-2672G>A|||||||rs3994810|1||1||SNV|HGNC|17164||||CCDS59447.1|ENSP00000347133||E9PDD6|UPI0000246DFE||Ensembl|G|G||||||||||||||||||||||||||||||||||||||,A|intron_variant&non_coding_transcript_variant|MODIFIER|BCL2L13|ENSG00000099968|Transcript|ENST00000399781|processed_transcript||3/4|ENST00000399781.1:n.823-2672G>A|||||||rs3994810|1||1||SNV|HGNC|17164||||||||||Ensembl|G|G||||||||||||||||||||||||||||||||||||||,A|intron_variant|MODIFIER|BCL2L13|ENSG00000099968|Transcript|ENST00000399782|protein_coding||3/6|ENST00000399782.1:c.122-2672G>A|||||||rs3994810|1||1||SNV|HGNC|17164|||||ENSP00000382682|Q9BXK5||UPI000002A4BC||Ensembl|G|G||||||||||||||||||||||||||||||||||||||,A|intron_variant|MODIFIER|BCL2L13|ENSG00000099968|Transcript|ENST00000418951|protein_coding||1/4|ENST00000418951.2:c.122-2672G>A|||||||rs3994810|1||1||SNV|HGNC|17164|||||ENSP00000410019||Q8IZP5|UPI00000740D0||Ensembl|G|G||||||||||||||||||||||||||||||||||||||,A|intron_variant&non_coding_transcript_variant|MODIFIER|BCL2L13|ENSG00000099968|Transcript|ENST00000464649|processed_transcript||1/3|ENST00000464649.1:n.131-2672G>A|||||||rs3994810|1||1||SNV|HGNC|17164||||||||||Ensembl|G|G||||||||||||||||||||||||||||||||||||||,A|intron_variant|MODIFIER|BCL2L13|ENSG00000099968|Transcript|ENST00000493680|protein_coding||2/5|ENST00000493680.1:c.122-2672G>A|||||||rs3994810|1||1||SNV|HGNC|17164|||||ENSP00000434764|Q9BXK5||UPI000002A4BC||Ensembl|G|G||||||||||||||||||||||||||||||||||||||,A|intron_variant&NMD_transcript_variant|MODIFIER|BCL2L13|ENSG00000099968|Transcript|ENST00000498133|nonsense_mediated_decay||2/5|ENST00000498133.1:c.122-2672G>A|||||||rs3994810|1||1||SNV|HGNC|17164|||||ENSP00000436321||F2Z2C3|UPI000155D5B6||Ensembl|G|G||||||||||||||||||||||||||||||||||||||,A|intron_variant|MODIFIER|BCL2L13|ENSG00000099968|Transcript|ENST00000538149|protein_coding||2/3|ENST00000538149.1:c.85-21701G>A|||||||rs3994810|1||1||SNV|HGNC|17164|||||ENSP00000441344||B7Z238|UPI0001914B19||Ensembl|G|G||||||||||||||||||||||||||||||||||||||,A|intron_variant|MODIFIER|BCL2L13|ENSG00000099968|Transcript|ENST00000543133|protein_coding||2/5|ENST00000543133.1:c.-208-2672G>A|||||||rs3994810|1||1||SNV|HGNC|17164||||CCDS59448.1|ENSP00000437667|Q9BXK5||UPI00001A3E35||Ensembl|G|G||||||||||||||||||||||||||||||||||||||,A|intron_variant|MODIFIER|BCL2L13|23786|Transcript|NM_001270726.1|protein_coding||1/5|NM_001270726.1:c.194-2672G>A|||||||rs3994810|1||1||SNV|EntrezGene|17164|||||NP_001257655.1|||||RefSeq|G|G||||||||||||||||||||||||||||||||||||||,A|intron_variant|MODIFIER|BCL2L13|23786|Transcript|NM_001270727.1|protein_coding||1/4|NM_001270727.1:c.194-2672G>A|||||||rs3994810|1||1||SNV|EntrezGene|17164|||||NP_001257656.1|||||RefSeq|G|G||||||||||||||||||||||||||||||||||||||,A|intron_variant|MODIFIER|BCL2L13|23786|Transcript|NM_001270728.1|protein_coding||2/3|NM_001270728.1:c.122-21701G>A|||||||rs3994810|1||1||SNV|EntrezGene|17164|||||NP_001257657.1|||||RefSeq|G|G||||||||||||||||||||||||||||||||||||||,A|intron_variant|MODIFIER|BCL2L13|23786|Transcript|NM_001270729.1|protein_coding||2/5|NM_001270729.1:c.-208-2672G>A|||||||rs3994810|1||1||SNV|EntrezGene|17164|||||NP_001257658.1|||||RefSeq|G|G||||||||||||||||||||||||||||||||||||||,A|intron_variant|MODIFIER|BCL2L13|23786|Transcript|NM_001270730.1|protein_coding||1/4|NM_001270730.1:c.-208-2672G>A|||||||rs3994810|1||1||SNV|EntrezGene|17164|||||NP_001257659.1|||||RefSeq|G|G||||||||||||||||||||||||||||||||||||||,A|intron_variant|MODIFIER|BCL2L13|23786|Transcript|NM_001270731.1|protein_coding||2/5|NM_001270731.1:c.-295-2672G>A|||||||rs3994810|1||1||SNV|EntrezGene|17164|||||NP_001257660.1|||||RefSeq|G|G||||||||||||||||||||||||||||||||||||||,A|intron_variant|MODIFIER|BCL2L13|23786|Transcript|NM_001270732.1|protein_coding||2/4|NM_001270732.1:c.122-2672G>A|||||||rs3994810|1||1||SNV|EntrezGene|17164|||||NP_001257661.1|||||RefSeq|G|G||||||||||||||||||||||||||||||||||||||,A|intron_variant|MODIFIER|BCL2L13|23786|Transcript|NM_001270734.1|protein_coding||2/4|NM_001270734.1:c.122-2672G>A|||||||rs3994810|1||1||SNV|EntrezGene|17164|||||NP_001257663.1|||||RefSeq|G|G||||||||||||||||||||||||||||||||||||||,A|intron_variant|MODIFIER|BCL2L13|23786|Transcript|NM_001270735.1|protein_coding||2/3|NM_001270735.1:c.122-2672G>A|||||||rs3994810|1||1||SNV|EntrezGene|17164|||||NP_001257664.1|||||RefSeq|G|G||||||||||||||||||||||||||||||||||||||,A|intron_variant|MODIFIER|BCL2L13|23786|Transcript|NM_015367.3|protein_coding||2/6|NM_015367.3:c.122-2672G>A|||||||rs3994810|1||1||SNV|EntrezGene|17164|||||NP_056182.2|||||RefSeq|G|G||||||||||||||||||||||||||||||||||||||,A|intron_variant&non_coding_transcript_variant|MODIFIER|BCL2L13|23786|Transcript|NR_073068.1|misc_RNA||2/4|NR_073068.1:n.287-2672G>A|||||||rs3994810|1||1||SNV|EntrezGene|17164||||||||||RefSeq|G|G||||||||||||||||||||||||||||||||||||||,A|intron_variant&non_coding_transcript_variant|MODIFIER|BCL2L13|23786|Transcript|NR_073069.1|misc_RNA||1/4|NR_073069.1:n.172-2672G>A|||||||rs3994810|1||1||SNV|EntrezGene|17164||||||||||RefSeq|G|G||||||||||||||||||||||||||||||||||||||,A|intron_variant|MODIFIER|BCL2L13|23786|Transcript|XM_005261231.1|protein_coding||2/6|XM_005261231.1:c.194-2672G>A|||||||rs3994810|1||1||SNV|EntrezGene|17164|YES||||XP_005261288.1|||||RefSeq|G|G||||||||||||||||||||||||||||||||||||||,A|intron_variant|MODIFIER|BCL2L13|23786|Transcript|XM_005261232.1|protein_coding||2/5|XM_005261232.1:c.122-2672G>A|||||||rs3994810|1||1||SNV|EntrezGene|17164|||||XP_005261289.1|||||RefSeq|G|G||||||||||||||||||||||||||||||||||||||,A|intron_variant|MODIFIER|BCL2L13|23786|Transcript|XM_005261233.1|protein_coding||3/5|XM_005261233.1:c.122-2672G>A|||||||rs3994810|1||1||SNV|EntrezGene|17164|||||XP_005261290.1|||||RefSeq|G|G|||||||||||||||||||||||||||||||||||||| +22 18167478 22:31314 T C 84068 PASS AC=365;AF=0.608;AN=600;BaseQRankSum=-1.48;ClippingRankSum=0.025;DP=5798;FS=0;GQ_MEAN=99.01;GQ_STDDEV=72.3;HW=1.6;InbreedingCoeff=0.0153;MLEAC=368;MLEAF=0.613;MQ=60;MQ0=0;MQRankSum=-0.045;NCC=0;POSITIVE_TRAIN_SITE;QD=19.03;ReadPosRankSum=0.143;SOR=0.641;VQSLOD=2.38;culprit=FS;CSQ=C|intron_variant|MODIFIER|BCL2L13|ENSG00000099968|Transcript|ENST00000317582|protein_coding||3/6|ENST00000317582.5:c.229+1391T>C|||||||rs5747326|1||1||SNV|HGNC|17164|YES|||CCDS13746.1|ENSP00000318883|Q9BXK5|B2RB43|UPI000004F301||Ensembl|T|T|||||||||0.7821|0.7133|0.8502|0.6501|0.7127|||0.713|0.7701|0.7356|0.6607|0.8534|0.6225|0.6667|0.677|0.7406|0.8534|gnomAD_EAS||||||||||||,C|intron_variant|MODIFIER|BCL2L13|ENSG00000099968|Transcript|ENST00000337612|protein_coding||3/4|ENST00000337612.5:c.-31+1391T>C|||||||rs5747326|1||1||SNV|HGNC|17164||||CCDS59448.1|ENSP00000338932|Q9BXK5||UPI00001A3E35||Ensembl|T|T|||||||||0.7821|0.7133|0.8502|0.6501|0.7127|||0.713|0.7701|0.7356|0.6607|0.8534|0.6225|0.6667|0.677|0.7406|0.8534|gnomAD_EAS||||||||||||,C|intron_variant|MODIFIER|BCL2L13|ENSG00000099968|Transcript|ENST00000355028|protein_coding||3/4|ENST00000355028.3:c.229+1391T>C|||||||rs5747326|1||1||SNV|HGNC|17164||||CCDS59447.1|ENSP00000347133||E9PDD6|UPI0000246DFE||Ensembl|T|T|||||||||0.7821|0.7133|0.8502|0.6501|0.7127|||0.713|0.7701|0.7356|0.6607|0.8534|0.6225|0.6667|0.677|0.7406|0.8534|gnomAD_EAS||||||||||||,C|upstream_gene_variant|MODIFIER|BCL2L13|ENSG00000099968|Transcript|ENST00000399777|nonsense_mediated_decay||||||||||rs5747326|1|4362|1|cds_start_NF|SNV|HGNC|17164|||||ENSP00000382677|||UPI0001F77C70||Ensembl|T|T|||||||||0.7821|0.7133|0.8502|0.6501|0.7127|||0.713|0.7701|0.7356|0.6607|0.8534|0.6225|0.6667|0.677|0.7406|0.8534|gnomAD_EAS||||||||||||,C|intron_variant&non_coding_transcript_variant|MODIFIER|BCL2L13|ENSG00000099968|Transcript|ENST00000399781|processed_transcript||4/4|ENST00000399781.1:n.930+1391T>C|||||||rs5747326|1||1||SNV|HGNC|17164||||||||||Ensembl|T|T|||||||||0.7821|0.7133|0.8502|0.6501|0.7127|||0.713|0.7701|0.7356|0.6607|0.8534|0.6225|0.6667|0.677|0.7406|0.8534|gnomAD_EAS||||||||||||,C|intron_variant|MODIFIER|BCL2L13|ENSG00000099968|Transcript|ENST00000399782|protein_coding||4/6|ENST00000399782.1:c.229+1391T>C|||||||rs5747326|1||1||SNV|HGNC|17164|||||ENSP00000382682|Q9BXK5||UPI000002A4BC||Ensembl|T|T|||||||||0.7821|0.7133|0.8502|0.6501|0.7127|||0.713|0.7701|0.7356|0.6607|0.8534|0.6225|0.6667|0.677|0.7406|0.8534|gnomAD_EAS||||||||||||,C|splice_region_variant&intron_variant|LOW|BCL2L13|ENSG00000099968|Transcript|ENST00000418951|protein_coding||3/4|ENST00000418951.2:c.*12+6T>C|||||||rs5747326|1||1||SNV|HGNC|17164|||||ENSP00000410019||Q8IZP5|UPI00000740D0||Ensembl|T|T|||||||||0.7821|0.7133|0.8502|0.6501|0.7127|||0.713|0.7701|0.7356|0.6607|0.8534|0.6225|0.6667|0.677|0.7406|0.8534|gnomAD_EAS||||||||||||,C|intron_variant&non_coding_transcript_variant|MODIFIER|BCL2L13|ENSG00000099968|Transcript|ENST00000464649|processed_transcript||2/3|ENST00000464649.1:n.238+1391T>C|||||||rs5747326|1||1||SNV|HGNC|17164||||||||||Ensembl|T|T|||||||||0.7821|0.7133|0.8502|0.6501|0.7127|||0.713|0.7701|0.7356|0.6607|0.8534|0.6225|0.6667|0.677|0.7406|0.8534|gnomAD_EAS||||||||||||,C|intron_variant|MODIFIER|BCL2L13|ENSG00000099968|Transcript|ENST00000493680|protein_coding||3/5|ENST00000493680.1:c.229+1391T>C|||||||rs5747326|1||1||SNV|HGNC|17164|||||ENSP00000434764|Q9BXK5||UPI000002A4BC||Ensembl|T|T|||||||||0.7821|0.7133|0.8502|0.6501|0.7127|||0.713|0.7701|0.7356|0.6607|0.8534|0.6225|0.6667|0.677|0.7406|0.8534|gnomAD_EAS||||||||||||,C|intron_variant&NMD_transcript_variant|MODIFIER|BCL2L13|ENSG00000099968|Transcript|ENST00000498133|nonsense_mediated_decay||3/5|ENST00000498133.1:c.229+1391T>C|||||||rs5747326|1||1||SNV|HGNC|17164|||||ENSP00000436321||F2Z2C3|UPI000155D5B6||Ensembl|T|T|||||||||0.7821|0.7133|0.8502|0.6501|0.7127|||0.713|0.7701|0.7356|0.6607|0.8534|0.6225|0.6667|0.677|0.7406|0.8534|gnomAD_EAS||||||||||||,C|intron_variant|MODIFIER|BCL2L13|ENSG00000099968|Transcript|ENST00000538149|protein_coding||2/3|ENST00000538149.1:c.85-17531T>C|||||||rs5747326|1||1||SNV|HGNC|17164|||||ENSP00000441344||B7Z238|UPI0001914B19||Ensembl|T|T|||||||||0.7821|0.7133|0.8502|0.6501|0.7127|||0.713|0.7701|0.7356|0.6607|0.8534|0.6225|0.6667|0.677|0.7406|0.8534|gnomAD_EAS||||||||||||,C|intron_variant|MODIFIER|BCL2L13|ENSG00000099968|Transcript|ENST00000543133|protein_coding||3/5|ENST00000543133.1:c.-101+1391T>C|||||||rs5747326|1||1||SNV|HGNC|17164||||CCDS59448.1|ENSP00000437667|Q9BXK5||UPI00001A3E35||Ensembl|T|T|||||||||0.7821|0.7133|0.8502|0.6501|0.7127|||0.713|0.7701|0.7356|0.6607|0.8534|0.6225|0.6667|0.677|0.7406|0.8534|gnomAD_EAS||||||||||||,C|intron_variant|MODIFIER|BCL2L13|23786|Transcript|NM_001270726.1|protein_coding||2/5|NM_001270726.1:c.301+1391T>C|||||||rs5747326|1||1||SNV|EntrezGene|17164|||||NP_001257655.1|||||RefSeq|T|T|||||||||0.7821|0.7133|0.8502|0.6501|0.7127|||0.713|0.7701|0.7356|0.6607|0.8534|0.6225|0.6667|0.677|0.7406|0.8534|gnomAD_EAS||||||||||||,C|intron_variant|MODIFIER|BCL2L13|23786|Transcript|NM_001270727.1|protein_coding||2/4|NM_001270727.1:c.301+1391T>C|||||||rs5747326|1||1||SNV|EntrezGene|17164|||||NP_001257656.1|||||RefSeq|T|T|||||||||0.7821|0.7133|0.8502|0.6501|0.7127|||0.713|0.7701|0.7356|0.6607|0.8534|0.6225|0.6667|0.677|0.7406|0.8534|gnomAD_EAS||||||||||||,C|intron_variant|MODIFIER|BCL2L13|23786|Transcript|NM_001270728.1|protein_coding||2/3|NM_001270728.1:c.122-17531T>C|||||||rs5747326|1||1||SNV|EntrezGene|17164|||||NP_001257657.1|||||RefSeq|T|T|||||||||0.7821|0.7133|0.8502|0.6501|0.7127|||0.713|0.7701|0.7356|0.6607|0.8534|0.6225|0.6667|0.677|0.7406|0.8534|gnomAD_EAS||||||||||||,C|intron_variant|MODIFIER|BCL2L13|23786|Transcript|NM_001270729.1|protein_coding||3/5|NM_001270729.1:c.-101+1391T>C|||||||rs5747326|1||1||SNV|EntrezGene|17164|||||NP_001257658.1|||||RefSeq|T|T|||||||||0.7821|0.7133|0.8502|0.6501|0.7127|||0.713|0.7701|0.7356|0.6607|0.8534|0.6225|0.6667|0.677|0.7406|0.8534|gnomAD_EAS||||||||||||,C|intron_variant|MODIFIER|BCL2L13|23786|Transcript|NM_001270730.1|protein_coding||2/4|NM_001270730.1:c.-101+1391T>C|||||||rs5747326|1||1||SNV|EntrezGene|17164|||||NP_001257659.1|||||RefSeq|T|T|||||||||0.7821|0.7133|0.8502|0.6501|0.7127|||0.713|0.7701|0.7356|0.6607|0.8534|0.6225|0.6667|0.677|0.7406|0.8534|gnomAD_EAS||||||||||||,C|intron_variant|MODIFIER|BCL2L13|23786|Transcript|NM_001270731.1|protein_coding||3/5|NM_001270731.1:c.-188+1391T>C|||||||rs5747326|1||1||SNV|EntrezGene|17164|||||NP_001257660.1|||||RefSeq|T|T|||||||||0.7821|0.7133|0.8502|0.6501|0.7127|||0.713|0.7701|0.7356|0.6607|0.8534|0.6225|0.6667|0.677|0.7406|0.8534|gnomAD_EAS||||||||||||,C|intron_variant|MODIFIER|BCL2L13|23786|Transcript|NM_001270732.1|protein_coding||3/4|NM_001270732.1:c.229+1391T>C|||||||rs5747326|1||1||SNV|EntrezGene|17164|||||NP_001257661.1|||||RefSeq|T|T|||||||||0.7821|0.7133|0.8502|0.6501|0.7127|||0.713|0.7701|0.7356|0.6607|0.8534|0.6225|0.6667|0.677|0.7406|0.8534|gnomAD_EAS||||||||||||,C|intron_variant|MODIFIER|BCL2L13|23786|Transcript|NM_001270734.1|protein_coding||3/4|NM_001270734.1:c.229+1391T>C|||||||rs5747326|1||1||SNV|EntrezGene|17164|||||NP_001257663.1|||||RefSeq|T|T|||||||||0.7821|0.7133|0.8502|0.6501|0.7127|||0.713|0.7701|0.7356|0.6607|0.8534|0.6225|0.6667|0.677|0.7406|0.8534|gnomAD_EAS||||||||||||,C|intron_variant|MODIFIER|BCL2L13|23786|Transcript|NM_001270735.1|protein_coding||3/3|NM_001270735.1:c.229+1391T>C|||||||rs5747326|1||1||SNV|EntrezGene|17164|||||NP_001257664.1|||||RefSeq|T|T|||||||||0.7821|0.7133|0.8502|0.6501|0.7127|||0.713|0.7701|0.7356|0.6607|0.8534|0.6225|0.6667|0.677|0.7406|0.8534|gnomAD_EAS||||||||||||,C|intron_variant|MODIFIER|BCL2L13|23786|Transcript|NM_015367.3|protein_coding||3/6|NM_015367.3:c.229+1391T>C|||||||rs5747326|1||1||SNV|EntrezGene|17164|||||NP_056182.2|||||RefSeq|T|T|||||||||0.7821|0.7133|0.8502|0.6501|0.7127|||0.713|0.7701|0.7356|0.6607|0.8534|0.6225|0.6667|0.677|0.7406|0.8534|gnomAD_EAS||||||||||||,C|intron_variant&non_coding_transcript_variant|MODIFIER|BCL2L13|23786|Transcript|NR_073068.1|misc_RNA||3/4|NR_073068.1:n.394+1391T>C|||||||rs5747326|1||1||SNV|EntrezGene|17164||||||||||RefSeq|T|T|||||||||0.7821|0.7133|0.8502|0.6501|0.7127|||0.713|0.7701|0.7356|0.6607|0.8534|0.6225|0.6667|0.677|0.7406|0.8534|gnomAD_EAS||||||||||||,C|splice_region_variant&intron_variant&non_coding_transcript_variant|LOW|BCL2L13|23786|Transcript|NR_073069.1|misc_RNA||3/4|NR_073069.1:n.377+6T>C|||||||rs5747326|1||1||SNV|EntrezGene|17164||||||||||RefSeq|T|T|||||||||0.7821|0.7133|0.8502|0.6501|0.7127|||0.713|0.7701|0.7356|0.6607|0.8534|0.6225|0.6667|0.677|0.7406|0.8534|gnomAD_EAS||||||||||||,C|intron_variant|MODIFIER|BCL2L13|23786|Transcript|XM_005261231.1|protein_coding||3/6|XM_005261231.1:c.301+1391T>C|||||||rs5747326|1||1||SNV|EntrezGene|17164|YES||||XP_005261288.1|||||RefSeq|T|T|||||||||0.7821|0.7133|0.8502|0.6501|0.7127|||0.713|0.7701|0.7356|0.6607|0.8534|0.6225|0.6667|0.677|0.7406|0.8534|gnomAD_EAS||||||||||||,C|intron_variant|MODIFIER|BCL2L13|23786|Transcript|XM_005261232.1|protein_coding||3/5|XM_005261232.1:c.229+1391T>C|||||||rs5747326|1||1||SNV|EntrezGene|17164|||||XP_005261289.1|||||RefSeq|T|T|||||||||0.7821|0.7133|0.8502|0.6501|0.7127|||0.713|0.7701|0.7356|0.6607|0.8534|0.6225|0.6667|0.677|0.7406|0.8534|gnomAD_EAS||||||||||||,C|intron_variant|MODIFIER|BCL2L13|23786|Transcript|XM_005261233.1|protein_coding||4/5|XM_005261233.1:c.229+1391T>C|||||||rs5747326|1||1||SNV|EntrezGene|17164|||||XP_005261290.1|||||RefSeq|T|T|||||||||0.7821|0.7133|0.8502|0.6501|0.7127|||0.713|0.7701|0.7356|0.6607|0.8534|0.6225|0.6667|0.677|0.7406|0.8534|gnomAD_EAS||||||||||||,C|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000143556|promoter_flanking_region||||||||||rs5747326|1||||SNV|||||||||||||||||||||||0.7821|0.7133|0.8502|0.6501|0.7127|||0.713|0.7701|0.7356|0.6607|0.8534|0.6225|0.6667|0.677|0.7406|0.8534|gnomAD_EAS|||||||||||| +22 18184011 22:31473 G A 289332 PASS AC=524;AF=0.873;AN=600;BaseQRankSum=0.919;ClippingRankSum=0.106;DP=10746;FS=0;GQ_MEAN=170.44;GQ_STDDEV=125.89;HW=12;InbreedingCoeff=-0.1149;MLEAC=524;MLEAF=0.873;MQ=60;MQ0=0;MQRankSum=0.266;NCC=0;POSITIVE_TRAIN_SITE;QD=27.42;ReadPosRankSum=0.361;SOR=0.617;VQSLOD=3.7;culprit=FS;CSQ=A|intron_variant|MODIFIER|BCL2L13|ENSG00000099968|Transcript|ENST00000317582|protein_coding||5/6|ENST00000317582.5:c.457-998G>A|||||||rs2587082|1||1||SNV|HGNC|17164|YES|||CCDS13746.1|ENSP00000318883|Q9BXK5|B2RB43|UPI000004F301||Ensembl|G|G||||||||0.8586|0.9085|0.8516|0.9375|0.8121|0.7628||||||||||||0.9375|EAS||||||||||||,A|intron_variant|MODIFIER|BCL2L13|ENSG00000099968|Transcript|ENST00000337612|protein_coding||3/4|ENST00000337612.5:c.-30-998G>A|||||||rs2587082|1||1||SNV|HGNC|17164||||CCDS59448.1|ENSP00000338932|Q9BXK5||UPI00001A3E35||Ensembl|G|G||||||||0.8586|0.9085|0.8516|0.9375|0.8121|0.7628||||||||||||0.9375|EAS||||||||||||,A|intron_variant|MODIFIER|BCL2L13|ENSG00000099968|Transcript|ENST00000355028|protein_coding||4/4|ENST00000355028.3:c.386+12103G>A|||||||rs2587082|1||1||SNV|HGNC|17164||||CCDS59447.1|ENSP00000347133||E9PDD6|UPI0000246DFE||Ensembl|G|G||||||||0.8586|0.9085|0.8516|0.9375|0.8121|0.7628||||||||||||0.9375|EAS||||||||||||,A|intron_variant&NMD_transcript_variant|MODIFIER|BCL2L13|ENSG00000099968|Transcript|ENST00000399777|nonsense_mediated_decay||1/2|ENST00000399777.1:c.70-998G>A|||||||rs2587082|1||1|cds_start_NF|SNV|HGNC|17164|||||ENSP00000382677|||UPI0001F77C70||Ensembl|G|G||||||||0.8586|0.9085|0.8516|0.9375|0.8121|0.7628||||||||||||0.9375|EAS||||||||||||,A|intron_variant|MODIFIER|BCL2L13|ENSG00000099968|Transcript|ENST00000399782|protein_coding||6/6|ENST00000399782.1:c.457-998G>A|||||||rs2587082|1||1||SNV|HGNC|17164|||||ENSP00000382682|Q9BXK5||UPI000002A4BC||Ensembl|G|G||||||||0.8586|0.9085|0.8516|0.9375|0.8121|0.7628||||||||||||0.9375|EAS||||||||||||,A|intron_variant|MODIFIER|BCL2L13|ENSG00000099968|Transcript|ENST00000418951|protein_coding||4/4|ENST00000418951.2:c.*169+12103G>A|||||||rs2587082|1||1||SNV|HGNC|17164|||||ENSP00000410019||Q8IZP5|UPI00000740D0||Ensembl|G|G||||||||0.8586|0.9085|0.8516|0.9375|0.8121|0.7628||||||||||||0.9375|EAS||||||||||||,A|intron_variant&non_coding_transcript_variant|MODIFIER|BCL2L13|ENSG00000099968|Transcript|ENST00000479296|processed_transcript||1/1|ENST00000479296.1:n.474-998G>A|||||||rs2587082|1||1||SNV|HGNC|17164||||||||||Ensembl|G|G||||||||0.8586|0.9085|0.8516|0.9375|0.8121|0.7628||||||||||||0.9375|EAS||||||||||||,A|intron_variant|MODIFIER|BCL2L13|ENSG00000099968|Transcript|ENST00000493680|protein_coding||5/5|ENST00000493680.1:c.457-998G>A|||||||rs2587082|1||1||SNV|HGNC|17164|||||ENSP00000434764|Q9BXK5||UPI000002A4BC||Ensembl|G|G||||||||0.8586|0.9085|0.8516|0.9375|0.8121|0.7628||||||||||||0.9375|EAS||||||||||||,A|intron_variant&NMD_transcript_variant|MODIFIER|BCL2L13|ENSG00000099968|Transcript|ENST00000498133|nonsense_mediated_decay||4/5|ENST00000498133.1:c.*63-998G>A|||||||rs2587082|1||1||SNV|HGNC|17164|||||ENSP00000436321||F2Z2C3|UPI000155D5B6||Ensembl|G|G||||||||0.8586|0.9085|0.8516|0.9375|0.8121|0.7628||||||||||||0.9375|EAS||||||||||||,A|intron_variant|MODIFIER|BCL2L13|ENSG00000099968|Transcript|ENST00000538149|protein_coding||2/3|ENST00000538149.1:c.85-998G>A|||||||rs2587082|1||1||SNV|HGNC|17164|||||ENSP00000441344||B7Z238|UPI0001914B19||Ensembl|G|G||||||||0.8586|0.9085|0.8516|0.9375|0.8121|0.7628||||||||||||0.9375|EAS||||||||||||,A|intron_variant|MODIFIER|BCL2L13|ENSG00000099968|Transcript|ENST00000543133|protein_coding||4/5|ENST00000543133.1:c.-30-998G>A|||||||rs2587082|1||1||SNV|HGNC|17164||||CCDS59448.1|ENSP00000437667|Q9BXK5||UPI00001A3E35||Ensembl|G|G||||||||0.8586|0.9085|0.8516|0.9375|0.8121|0.7628||||||||||||0.9375|EAS||||||||||||,A|intron_variant|MODIFIER|BCL2L13|23786|Transcript|NM_001270726.1|protein_coding||4/5|NM_001270726.1:c.529-998G>A|||||||rs2587082|1||1||SNV|EntrezGene|17164|||||NP_001257655.1|||||RefSeq|G|G||||||||0.8586|0.9085|0.8516|0.9375|0.8121|0.7628||||||||||||0.9375|EAS||||||||||||,A|intron_variant|MODIFIER|BCL2L13|23786|Transcript|NM_001270727.1|protein_coding||4/4|NM_001270727.1:c.528+5035G>A|||||||rs2587082|1||1||SNV|EntrezGene|17164|||||NP_001257656.1|||||RefSeq|G|G||||||||0.8586|0.9085|0.8516|0.9375|0.8121|0.7628||||||||||||0.9375|EAS||||||||||||,A|intron_variant|MODIFIER|BCL2L13|23786|Transcript|NM_001270728.1|protein_coding||2/3|NM_001270728.1:c.122-998G>A|||||||rs2587082|1||1||SNV|EntrezGene|17164|||||NP_001257657.1|||||RefSeq|G|G||||||||0.8586|0.9085|0.8516|0.9375|0.8121|0.7628||||||||||||0.9375|EAS||||||||||||,A|intron_variant|MODIFIER|BCL2L13|23786|Transcript|NM_001270729.1|protein_coding||4/5|NM_001270729.1:c.-30-998G>A|||||||rs2587082|1||1||SNV|EntrezGene|17164|||||NP_001257658.1|||||RefSeq|G|G||||||||0.8586|0.9085|0.8516|0.9375|0.8121|0.7628||||||||||||0.9375|EAS||||||||||||,A|intron_variant|MODIFIER|BCL2L13|23786|Transcript|NM_001270730.1|protein_coding||3/4|NM_001270730.1:c.-30-998G>A|||||||rs2587082|1||1||SNV|EntrezGene|17164|||||NP_001257659.1|||||RefSeq|G|G||||||||0.8586|0.9085|0.8516|0.9375|0.8121|0.7628||||||||||||0.9375|EAS||||||||||||,A|intron_variant|MODIFIER|BCL2L13|23786|Transcript|NM_001270731.1|protein_coding||4/5|NM_001270731.1:c.-30-998G>A|||||||rs2587082|1||1||SNV|EntrezGene|17164|||||NP_001257660.1|||||RefSeq|G|G||||||||0.8586|0.9085|0.8516|0.9375|0.8121|0.7628||||||||||||0.9375|EAS||||||||||||,A|intron_variant|MODIFIER|BCL2L13|23786|Transcript|NM_001270732.1|protein_coding||3/4|NM_001270732.1:c.230-998G>A|||||||rs2587082|1||1||SNV|EntrezGene|17164|||||NP_001257661.1|||||RefSeq|G|G||||||||0.8586|0.9085|0.8516|0.9375|0.8121|0.7628||||||||||||0.9375|EAS||||||||||||,A|intron_variant|MODIFIER|BCL2L13|23786|Transcript|NM_001270734.1|protein_coding||4/4|NM_001270734.1:c.386+12103G>A|||||||rs2587082|1||1||SNV|EntrezGene|17164|||||NP_001257663.1|||||RefSeq|G|G||||||||0.8586|0.9085|0.8516|0.9375|0.8121|0.7628||||||||||||0.9375|EAS||||||||||||,A|intron_variant|MODIFIER|BCL2L13|23786|Transcript|NM_001270735.1|protein_coding||3/3|NM_001270735.1:c.229+17924G>A|||||||rs2587082|1||1||SNV|EntrezGene|17164|||||NP_001257664.1|||||RefSeq|G|G||||||||0.8586|0.9085|0.8516|0.9375|0.8121|0.7628||||||||||||0.9375|EAS||||||||||||,A|intron_variant|MODIFIER|BCL2L13|23786|Transcript|NM_015367.3|protein_coding||5/6|NM_015367.3:c.457-998G>A|||||||rs2587082|1||1||SNV|EntrezGene|17164|||||NP_056182.2|||||RefSeq|G|G||||||||0.8586|0.9085|0.8516|0.9375|0.8121|0.7628||||||||||||0.9375|EAS||||||||||||,A|intron_variant&non_coding_transcript_variant|MODIFIER|BCL2L13|23786|Transcript|NR_073068.1|misc_RNA||4/4|NR_073068.1:n.551+12103G>A|||||||rs2587082|1||1||SNV|EntrezGene|17164||||||||||RefSeq|G|G||||||||0.8586|0.9085|0.8516|0.9375|0.8121|0.7628||||||||||||0.9375|EAS||||||||||||,A|intron_variant&non_coding_transcript_variant|MODIFIER|BCL2L13|23786|Transcript|NR_073069.1|misc_RNA||4/4|NR_073069.1:n.534+12103G>A|||||||rs2587082|1||1||SNV|EntrezGene|17164||||||||||RefSeq|G|G||||||||0.8586|0.9085|0.8516|0.9375|0.8121|0.7628||||||||||||0.9375|EAS||||||||||||,A|intron_variant|MODIFIER|BCL2L13|23786|Transcript|XM_005261231.1|protein_coding||5/6|XM_005261231.1:c.529-998G>A|||||||rs2587082|1||1||SNV|EntrezGene|17164|YES||||XP_005261288.1|||||RefSeq|G|G||||||||0.8586|0.9085|0.8516|0.9375|0.8121|0.7628||||||||||||0.9375|EAS||||||||||||,A|intron_variant|MODIFIER|BCL2L13|23786|Transcript|XM_005261232.1|protein_coding||5/5|XM_005261232.1:c.457-998G>A|||||||rs2587082|1||1||SNV|EntrezGene|17164|||||XP_005261289.1|||||RefSeq|G|G||||||||0.8586|0.9085|0.8516|0.9375|0.8121|0.7628||||||||||||0.9375|EAS||||||||||||,A|intron_variant|MODIFIER|BCL2L13|23786|Transcript|XM_005261233.1|protein_coding||4/5|XM_005261233.1:c.230-998G>A|||||||rs2587082|1||1||SNV|EntrezGene|17164|||||XP_005261290.1|||||RefSeq|G|G||||||||0.8586|0.9085|0.8516|0.9375|0.8121|0.7628||||||||||||0.9375|EAS|||||||||||| +22 18184290 22:31475 T C 242253 PASS AC=524;AF=0.873;AN=600;BaseQRankSum=-2.561;ClippingRankSum=-0.19;DP=10394;FS=0.846;GQ_MEAN=158.54;GQ_STDDEV=113.22;HW=12;InbreedingCoeff=-0.1149;MLEAC=524;MLEAF=0.873;MQ=60;MQ0=0;MQRankSum=-0.06;NCC=0;POSITIVE_TRAIN_SITE;QD=24.06;ReadPosRankSum=0.315;SOR=0.858;VQSLOD=3.93;culprit=SOR;CSQ=C|intron_variant|MODIFIER|BCL2L13|ENSG00000099968|Transcript|ENST00000317582|protein_coding||5/6|ENST00000317582.5:c.457-719T>C|||||||rs2587083|1||1||SNV|HGNC|17164|YES|||CCDS13746.1|ENSP00000318883|Q9BXK5|B2RB43|UPI000004F301||Ensembl|T|T|||||||||0.9864|0.8545|0.9375|0.8151|0.7628||||||||||||0.9864|AFR||||||||||||,C|intron_variant|MODIFIER|BCL2L13|ENSG00000099968|Transcript|ENST00000337612|protein_coding||3/4|ENST00000337612.5:c.-30-719T>C|||||||rs2587083|1||1||SNV|HGNC|17164||||CCDS59448.1|ENSP00000338932|Q9BXK5||UPI00001A3E35||Ensembl|T|T|||||||||0.9864|0.8545|0.9375|0.8151|0.7628||||||||||||0.9864|AFR||||||||||||,C|intron_variant|MODIFIER|BCL2L13|ENSG00000099968|Transcript|ENST00000355028|protein_coding||4/4|ENST00000355028.3:c.386+12382T>C|||||||rs2587083|1||1||SNV|HGNC|17164||||CCDS59447.1|ENSP00000347133||E9PDD6|UPI0000246DFE||Ensembl|T|T|||||||||0.9864|0.8545|0.9375|0.8151|0.7628||||||||||||0.9864|AFR||||||||||||,C|intron_variant&NMD_transcript_variant|MODIFIER|BCL2L13|ENSG00000099968|Transcript|ENST00000399777|nonsense_mediated_decay||1/2|ENST00000399777.1:c.70-719T>C|||||||rs2587083|1||1|cds_start_NF|SNV|HGNC|17164|||||ENSP00000382677|||UPI0001F77C70||Ensembl|T|T|||||||||0.9864|0.8545|0.9375|0.8151|0.7628||||||||||||0.9864|AFR||||||||||||,C|intron_variant|MODIFIER|BCL2L13|ENSG00000099968|Transcript|ENST00000399782|protein_coding||6/6|ENST00000399782.1:c.457-719T>C|||||||rs2587083|1||1||SNV|HGNC|17164|||||ENSP00000382682|Q9BXK5||UPI000002A4BC||Ensembl|T|T|||||||||0.9864|0.8545|0.9375|0.8151|0.7628||||||||||||0.9864|AFR||||||||||||,C|intron_variant|MODIFIER|BCL2L13|ENSG00000099968|Transcript|ENST00000418951|protein_coding||4/4|ENST00000418951.2:c.*169+12382T>C|||||||rs2587083|1||1||SNV|HGNC|17164|||||ENSP00000410019||Q8IZP5|UPI00000740D0||Ensembl|T|T|||||||||0.9864|0.8545|0.9375|0.8151|0.7628||||||||||||0.9864|AFR||||||||||||,C|intron_variant&non_coding_transcript_variant|MODIFIER|BCL2L13|ENSG00000099968|Transcript|ENST00000479296|processed_transcript||1/1|ENST00000479296.1:n.474-719T>C|||||||rs2587083|1||1||SNV|HGNC|17164||||||||||Ensembl|T|T|||||||||0.9864|0.8545|0.9375|0.8151|0.7628||||||||||||0.9864|AFR||||||||||||,C|intron_variant|MODIFIER|BCL2L13|ENSG00000099968|Transcript|ENST00000493680|protein_coding||5/5|ENST00000493680.1:c.457-719T>C|||||||rs2587083|1||1||SNV|HGNC|17164|||||ENSP00000434764|Q9BXK5||UPI000002A4BC||Ensembl|T|T|||||||||0.9864|0.8545|0.9375|0.8151|0.7628||||||||||||0.9864|AFR||||||||||||,C|intron_variant&NMD_transcript_variant|MODIFIER|BCL2L13|ENSG00000099968|Transcript|ENST00000498133|nonsense_mediated_decay||4/5|ENST00000498133.1:c.*63-719T>C|||||||rs2587083|1||1||SNV|HGNC|17164|||||ENSP00000436321||F2Z2C3|UPI000155D5B6||Ensembl|T|T|||||||||0.9864|0.8545|0.9375|0.8151|0.7628||||||||||||0.9864|AFR||||||||||||,C|intron_variant|MODIFIER|BCL2L13|ENSG00000099968|Transcript|ENST00000538149|protein_coding||2/3|ENST00000538149.1:c.85-719T>C|||||||rs2587083|1||1||SNV|HGNC|17164|||||ENSP00000441344||B7Z238|UPI0001914B19||Ensembl|T|T|||||||||0.9864|0.8545|0.9375|0.8151|0.7628||||||||||||0.9864|AFR||||||||||||,C|intron_variant|MODIFIER|BCL2L13|ENSG00000099968|Transcript|ENST00000543133|protein_coding||4/5|ENST00000543133.1:c.-30-719T>C|||||||rs2587083|1||1||SNV|HGNC|17164||||CCDS59448.1|ENSP00000437667|Q9BXK5||UPI00001A3E35||Ensembl|T|T|||||||||0.9864|0.8545|0.9375|0.8151|0.7628||||||||||||0.9864|AFR||||||||||||,C|intron_variant|MODIFIER|BCL2L13|23786|Transcript|NM_001270726.1|protein_coding||4/5|NM_001270726.1:c.529-719T>C|||||||rs2587083|1||1||SNV|EntrezGene|17164|||||NP_001257655.1|||||RefSeq|T|T|||||||||0.9864|0.8545|0.9375|0.8151|0.7628||||||||||||0.9864|AFR||||||||||||,C|intron_variant|MODIFIER|BCL2L13|23786|Transcript|NM_001270727.1|protein_coding||4/4|NM_001270727.1:c.528+5314T>C|||||||rs2587083|1||1||SNV|EntrezGene|17164|||||NP_001257656.1|||||RefSeq|T|T|||||||||0.9864|0.8545|0.9375|0.8151|0.7628||||||||||||0.9864|AFR||||||||||||,C|intron_variant|MODIFIER|BCL2L13|23786|Transcript|NM_001270728.1|protein_coding||2/3|NM_001270728.1:c.122-719T>C|||||||rs2587083|1||1||SNV|EntrezGene|17164|||||NP_001257657.1|||||RefSeq|T|T|||||||||0.9864|0.8545|0.9375|0.8151|0.7628||||||||||||0.9864|AFR||||||||||||,C|intron_variant|MODIFIER|BCL2L13|23786|Transcript|NM_001270729.1|protein_coding||4/5|NM_001270729.1:c.-30-719T>C|||||||rs2587083|1||1||SNV|EntrezGene|17164|||||NP_001257658.1|||||RefSeq|T|T|||||||||0.9864|0.8545|0.9375|0.8151|0.7628||||||||||||0.9864|AFR||||||||||||,C|intron_variant|MODIFIER|BCL2L13|23786|Transcript|NM_001270730.1|protein_coding||3/4|NM_001270730.1:c.-30-719T>C|||||||rs2587083|1||1||SNV|EntrezGene|17164|||||NP_001257659.1|||||RefSeq|T|T|||||||||0.9864|0.8545|0.9375|0.8151|0.7628||||||||||||0.9864|AFR||||||||||||,C|intron_variant|MODIFIER|BCL2L13|23786|Transcript|NM_001270731.1|protein_coding||4/5|NM_001270731.1:c.-30-719T>C|||||||rs2587083|1||1||SNV|EntrezGene|17164|||||NP_001257660.1|||||RefSeq|T|T|||||||||0.9864|0.8545|0.9375|0.8151|0.7628||||||||||||0.9864|AFR||||||||||||,C|intron_variant|MODIFIER|BCL2L13|23786|Transcript|NM_001270732.1|protein_coding||3/4|NM_001270732.1:c.230-719T>C|||||||rs2587083|1||1||SNV|EntrezGene|17164|||||NP_001257661.1|||||RefSeq|T|T|||||||||0.9864|0.8545|0.9375|0.8151|0.7628||||||||||||0.9864|AFR||||||||||||,C|intron_variant|MODIFIER|BCL2L13|23786|Transcript|NM_001270734.1|protein_coding||4/4|NM_001270734.1:c.386+12382T>C|||||||rs2587083|1||1||SNV|EntrezGene|17164|||||NP_001257663.1|||||RefSeq|T|T|||||||||0.9864|0.8545|0.9375|0.8151|0.7628||||||||||||0.9864|AFR||||||||||||,C|intron_variant|MODIFIER|BCL2L13|23786|Transcript|NM_001270735.1|protein_coding||3/3|NM_001270735.1:c.229+18203T>C|||||||rs2587083|1||1||SNV|EntrezGene|17164|||||NP_001257664.1|||||RefSeq|T|T|||||||||0.9864|0.8545|0.9375|0.8151|0.7628||||||||||||0.9864|AFR||||||||||||,C|intron_variant|MODIFIER|BCL2L13|23786|Transcript|NM_015367.3|protein_coding||5/6|NM_015367.3:c.457-719T>C|||||||rs2587083|1||1||SNV|EntrezGene|17164|||||NP_056182.2|||||RefSeq|T|T|||||||||0.9864|0.8545|0.9375|0.8151|0.7628||||||||||||0.9864|AFR||||||||||||,C|intron_variant&non_coding_transcript_variant|MODIFIER|BCL2L13|23786|Transcript|NR_073068.1|misc_RNA||4/4|NR_073068.1:n.551+12382T>C|||||||rs2587083|1||1||SNV|EntrezGene|17164||||||||||RefSeq|T|T|||||||||0.9864|0.8545|0.9375|0.8151|0.7628||||||||||||0.9864|AFR||||||||||||,C|intron_variant&non_coding_transcript_variant|MODIFIER|BCL2L13|23786|Transcript|NR_073069.1|misc_RNA||4/4|NR_073069.1:n.534+12382T>C|||||||rs2587083|1||1||SNV|EntrezGene|17164||||||||||RefSeq|T|T|||||||||0.9864|0.8545|0.9375|0.8151|0.7628||||||||||||0.9864|AFR||||||||||||,C|intron_variant|MODIFIER|BCL2L13|23786|Transcript|XM_005261231.1|protein_coding||5/6|XM_005261231.1:c.529-719T>C|||||||rs2587083|1||1||SNV|EntrezGene|17164|YES||||XP_005261288.1|||||RefSeq|T|T|||||||||0.9864|0.8545|0.9375|0.8151|0.7628||||||||||||0.9864|AFR||||||||||||,C|intron_variant|MODIFIER|BCL2L13|23786|Transcript|XM_005261232.1|protein_coding||5/5|XM_005261232.1:c.457-719T>C|||||||rs2587083|1||1||SNV|EntrezGene|17164|||||XP_005261289.1|||||RefSeq|T|T|||||||||0.9864|0.8545|0.9375|0.8151|0.7628||||||||||||0.9864|AFR||||||||||||,C|intron_variant|MODIFIER|BCL2L13|23786|Transcript|XM_005261233.1|protein_coding||4/5|XM_005261233.1:c.230-719T>C|||||||rs2587083|1||1||SNV|EntrezGene|17164|||||XP_005261290.1|||||RefSeq|T|T|||||||||0.9864|0.8545|0.9375|0.8151|0.7628||||||||||||0.9864|AFR|||||||||||| +22 18191951 22:31517 A G 190711 PASS AC=531;AF=0.885;AN=600;BaseQRankSum=-1.061;ClippingRankSum=0.158;DP=8191;FS=0;GQ_MEAN=110.31;GQ_STDDEV=78.83;HW=8.4;InbreedingCoeff=-0.0972;MLEAC=531;MLEAF=0.885;MQ=59.4;MQ0=0;MQRankSum=0.035;NCC=0;POSITIVE_TRAIN_SITE;QD=24.2;ReadPosRankSum=0.246;SOR=0.613;VQSLOD=3.94;culprit=FS;CSQ=G|intron_variant|MODIFIER|BCL2L13|ENSG00000099968|Transcript|ENST00000317582|protein_coding||6/6|ENST00000317582.5:c.600+6799A>G|||||||rs2535711|1||1||SNV|HGNC|17164|YES|||CCDS13746.1|ENSP00000318883|Q9BXK5|B2RB43|UPI000004F301||Ensembl|A|A|||||||||0.9289|0.853|0.9375|0.8151|0.7618||||||||||||0.9375|EAS||||||||||||,G|intron_variant|MODIFIER|BCL2L13|ENSG00000099968|Transcript|ENST00000337612|protein_coding||4/4|ENST00000337612.5:c.114+6799A>G|||||||rs2535711|1||1||SNV|HGNC|17164||||CCDS59448.1|ENSP00000338932|Q9BXK5||UPI00001A3E35||Ensembl|A|A|||||||||0.9289|0.853|0.9375|0.8151|0.7618||||||||||||0.9375|EAS||||||||||||,G|intron_variant|MODIFIER|BCL2L13|ENSG00000099968|Transcript|ENST00000355028|protein_coding||4/4|ENST00000355028.3:c.387-17492A>G|||||||rs2535711|1||1||SNV|HGNC|17164||||CCDS59447.1|ENSP00000347133||E9PDD6|UPI0000246DFE||Ensembl|A|A|||||||||0.9289|0.853|0.9375|0.8151|0.7618||||||||||||0.9375|EAS||||||||||||,G|intron_variant&NMD_transcript_variant|MODIFIER|BCL2L13|ENSG00000099968|Transcript|ENST00000399777|nonsense_mediated_decay||2/2|ENST00000399777.1:c.*98+6799A>G|||||||rs2535711|1||1|cds_start_NF|SNV|HGNC|17164|||||ENSP00000382677|||UPI0001F77C70||Ensembl|A|A|||||||||0.9289|0.853|0.9375|0.8151|0.7618||||||||||||0.9375|EAS||||||||||||,G|intron_variant|MODIFIER|BCL2L13|ENSG00000099968|Transcript|ENST00000418951|protein_coding||4/4|ENST00000418951.2:c.*170-17492A>G|||||||rs2535711|1||1||SNV|HGNC|17164|||||ENSP00000410019||Q8IZP5|UPI00000740D0||Ensembl|A|A|||||||||0.9289|0.853|0.9375|0.8151|0.7618||||||||||||0.9375|EAS||||||||||||,G|intron_variant&non_coding_transcript_variant|MODIFIER|BCL2L13|ENSG00000099968|Transcript|ENST00000485631|processed_transcript||1/1|ENST00000485631.1:n.116+2360A>G|||||||rs2535711|1||1||SNV|HGNC|17164||||||||||Ensembl|A|A|||||||||0.9289|0.853|0.9375|0.8151|0.7618||||||||||||0.9375|EAS||||||||||||,G|intron_variant&NMD_transcript_variant|MODIFIER|BCL2L13|ENSG00000099968|Transcript|ENST00000498133|nonsense_mediated_decay||5/5|ENST00000498133.1:c.*206+6799A>G|||||||rs2535711|1||1||SNV|HGNC|17164|||||ENSP00000436321||F2Z2C3|UPI000155D5B6||Ensembl|A|A|||||||||0.9289|0.853|0.9375|0.8151|0.7618||||||||||||0.9375|EAS||||||||||||,G|intron_variant|MODIFIER|BCL2L13|ENSG00000099968|Transcript|ENST00000538149|protein_coding||3/3|ENST00000538149.1:c.228+6799A>G|||||||rs2535711|1||1||SNV|HGNC|17164|||||ENSP00000441344||B7Z238|UPI0001914B19||Ensembl|A|A|||||||||0.9289|0.853|0.9375|0.8151|0.7618||||||||||||0.9375|EAS||||||||||||,G|intron_variant|MODIFIER|BCL2L13|ENSG00000099968|Transcript|ENST00000543133|protein_coding||5/5|ENST00000543133.1:c.114+6799A>G|||||||rs2535711|1||1||SNV|HGNC|17164||||CCDS59448.1|ENSP00000437667|Q9BXK5||UPI00001A3E35||Ensembl|A|A|||||||||0.9289|0.853|0.9375|0.8151|0.7618||||||||||||0.9375|EAS||||||||||||,G|intron_variant|MODIFIER|BCL2L13|23786|Transcript|NM_001270726.1|protein_coding||5/5|NM_001270726.1:c.672+6799A>G|||||||rs2535711|1||1||SNV|EntrezGene|17164|||||NP_001257655.1|||||RefSeq|A|A|||||||||0.9289|0.853|0.9375|0.8151|0.7618||||||||||||0.9375|EAS||||||||||||,G|intron_variant|MODIFIER|BCL2L13|23786|Transcript|NM_001270727.1|protein_coding||4/4|NM_001270727.1:c.528+12975A>G|||||||rs2535711|1||1||SNV|EntrezGene|17164|||||NP_001257656.1|||||RefSeq|A|A|||||||||0.9289|0.853|0.9375|0.8151|0.7618||||||||||||0.9375|EAS||||||||||||,G|intron_variant|MODIFIER|BCL2L13|23786|Transcript|NM_001270728.1|protein_coding||3/3|NM_001270728.1:c.265+6799A>G|||||||rs2535711|1||1||SNV|EntrezGene|17164|||||NP_001257657.1|||||RefSeq|A|A|||||||||0.9289|0.853|0.9375|0.8151|0.7618||||||||||||0.9375|EAS||||||||||||,G|intron_variant|MODIFIER|BCL2L13|23786|Transcript|NM_001270729.1|protein_coding||5/5|NM_001270729.1:c.114+6799A>G|||||||rs2535711|1||1||SNV|EntrezGene|17164|||||NP_001257658.1|||||RefSeq|A|A|||||||||0.9289|0.853|0.9375|0.8151|0.7618||||||||||||0.9375|EAS||||||||||||,G|intron_variant|MODIFIER|BCL2L13|23786|Transcript|NM_001270730.1|protein_coding||4/4|NM_001270730.1:c.114+6799A>G|||||||rs2535711|1||1||SNV|EntrezGene|17164|||||NP_001257659.1|||||RefSeq|A|A|||||||||0.9289|0.853|0.9375|0.8151|0.7618||||||||||||0.9375|EAS||||||||||||,G|intron_variant|MODIFIER|BCL2L13|23786|Transcript|NM_001270731.1|protein_coding||5/5|NM_001270731.1:c.114+6799A>G|||||||rs2535711|1||1||SNV|EntrezGene|17164|||||NP_001257660.1|||||RefSeq|A|A|||||||||0.9289|0.853|0.9375|0.8151|0.7618||||||||||||0.9375|EAS||||||||||||,G|intron_variant|MODIFIER|BCL2L13|23786|Transcript|NM_001270732.1|protein_coding||4/4|NM_001270732.1:c.373+6799A>G|||||||rs2535711|1||1||SNV|EntrezGene|17164|||||NP_001257661.1|||||RefSeq|A|A|||||||||0.9289|0.853|0.9375|0.8151|0.7618||||||||||||0.9375|EAS||||||||||||,G|intron_variant|MODIFIER|BCL2L13|23786|Transcript|NM_001270733.1|protein_coding||1/1|NM_001270733.1:c.-241+2360A>G|||||||rs2535711|1||1||SNV|EntrezGene|17164|||||NP_001257662.1|||||RefSeq|A|A|||||||||0.9289|0.853|0.9375|0.8151|0.7618||||||||||||0.9375|EAS||||||||||||,G|intron_variant|MODIFIER|BCL2L13|23786|Transcript|NM_001270734.1|protein_coding||4/4|NM_001270734.1:c.387-17492A>G|||||||rs2535711|1||1||SNV|EntrezGene|17164|||||NP_001257663.1|||||RefSeq|A|A|||||||||0.9289|0.853|0.9375|0.8151|0.7618||||||||||||0.9375|EAS||||||||||||,G|intron_variant|MODIFIER|BCL2L13|23786|Transcript|NM_001270735.1|protein_coding||3/3|NM_001270735.1:c.230-17492A>G|||||||rs2535711|1||1||SNV|EntrezGene|17164|||||NP_001257664.1|||||RefSeq|A|A|||||||||0.9289|0.853|0.9375|0.8151|0.7618||||||||||||0.9375|EAS||||||||||||,G|intron_variant|MODIFIER|BCL2L13|23786|Transcript|NM_015367.3|protein_coding||6/6|NM_015367.3:c.600+6799A>G|||||||rs2535711|1||1||SNV|EntrezGene|17164|||||NP_056182.2|||||RefSeq|A|A|||||||||0.9289|0.853|0.9375|0.8151|0.7618||||||||||||0.9375|EAS||||||||||||,G|intron_variant&non_coding_transcript_variant|MODIFIER|BCL2L13|23786|Transcript|NR_073068.1|misc_RNA||4/4|NR_073068.1:n.552-17492A>G|||||||rs2535711|1||1||SNV|EntrezGene|17164||||||||||RefSeq|A|A|||||||||0.9289|0.853|0.9375|0.8151|0.7618||||||||||||0.9375|EAS||||||||||||,G|intron_variant&non_coding_transcript_variant|MODIFIER|BCL2L13|23786|Transcript|NR_073069.1|misc_RNA||4/4|NR_073069.1:n.535-17492A>G|||||||rs2535711|1||1||SNV|EntrezGene|17164||||||||||RefSeq|A|A|||||||||0.9289|0.853|0.9375|0.8151|0.7618||||||||||||0.9375|EAS||||||||||||,G|intron_variant|MODIFIER|BCL2L13|23786|Transcript|XM_005261231.1|protein_coding||6/6|XM_005261231.1:c.672+6799A>G|||||||rs2535711|1||1||SNV|EntrezGene|17164|YES||||XP_005261288.1|||||RefSeq|A|A|||||||||0.9289|0.853|0.9375|0.8151|0.7618||||||||||||0.9375|EAS||||||||||||,G|intron_variant|MODIFIER|BCL2L13|23786|Transcript|XM_005261233.1|protein_coding||5/5|XM_005261233.1:c.373+6799A>G|||||||rs2535711|1||1||SNV|EntrezGene|17164|||||XP_005261290.1|||||RefSeq|A|A|||||||||0.9289|0.853|0.9375|0.8151|0.7618||||||||||||0.9375|EAS|||||||||||| +22 18192136 22:31518 A G 238291 PASS AC=531;AF=0.885;AN=600;BaseQRankSum=-2.317;ClippingRankSum=-0.205;DP=9824;FS=0;GQ_MEAN=142.78;GQ_STDDEV=109.18;HW=8.4;InbreedingCoeff=-0.0972;MLEAC=531;MLEAF=0.885;MQ=60;MQ0=0;MQRankSum=-0.037;NCC=0;POSITIVE_TRAIN_SITE;QD=25.06;ReadPosRankSum=0.154;SOR=0.624;VQSLOD=4.27;culprit=FS;CSQ=G|intron_variant|MODIFIER|BCL2L13|ENSG00000099968|Transcript|ENST00000317582|protein_coding||6/6|ENST00000317582.5:c.600+6984A>G|||||||rs2535712|1||1||SNV|HGNC|17164|YES|||CCDS13746.1|ENSP00000318883|Q9BXK5|B2RB43|UPI000004F301||Ensembl|A|A||||||||0.8582|0.907|0.8516|0.9375|0.8121|0.7628||||||||||||0.9375|EAS||||||||||||,G|intron_variant|MODIFIER|BCL2L13|ENSG00000099968|Transcript|ENST00000337612|protein_coding||4/4|ENST00000337612.5:c.114+6984A>G|||||||rs2535712|1||1||SNV|HGNC|17164||||CCDS59448.1|ENSP00000338932|Q9BXK5||UPI00001A3E35||Ensembl|A|A||||||||0.8582|0.907|0.8516|0.9375|0.8121|0.7628||||||||||||0.9375|EAS||||||||||||,G|intron_variant|MODIFIER|BCL2L13|ENSG00000099968|Transcript|ENST00000355028|protein_coding||4/4|ENST00000355028.3:c.387-17307A>G|||||||rs2535712|1||1||SNV|HGNC|17164||||CCDS59447.1|ENSP00000347133||E9PDD6|UPI0000246DFE||Ensembl|A|A||||||||0.8582|0.907|0.8516|0.9375|0.8121|0.7628||||||||||||0.9375|EAS||||||||||||,G|intron_variant&NMD_transcript_variant|MODIFIER|BCL2L13|ENSG00000099968|Transcript|ENST00000399777|nonsense_mediated_decay||2/2|ENST00000399777.1:c.*98+6984A>G|||||||rs2535712|1||1|cds_start_NF|SNV|HGNC|17164|||||ENSP00000382677|||UPI0001F77C70||Ensembl|A|A||||||||0.8582|0.907|0.8516|0.9375|0.8121|0.7628||||||||||||0.9375|EAS||||||||||||,G|intron_variant|MODIFIER|BCL2L13|ENSG00000099968|Transcript|ENST00000418951|protein_coding||4/4|ENST00000418951.2:c.*170-17307A>G|||||||rs2535712|1||1||SNV|HGNC|17164|||||ENSP00000410019||Q8IZP5|UPI00000740D0||Ensembl|A|A||||||||0.8582|0.907|0.8516|0.9375|0.8121|0.7628||||||||||||0.9375|EAS||||||||||||,G|intron_variant&non_coding_transcript_variant|MODIFIER|BCL2L13|ENSG00000099968|Transcript|ENST00000485631|processed_transcript||1/1|ENST00000485631.1:n.116+2545A>G|||||||rs2535712|1||1||SNV|HGNC|17164||||||||||Ensembl|A|A||||||||0.8582|0.907|0.8516|0.9375|0.8121|0.7628||||||||||||0.9375|EAS||||||||||||,G|intron_variant&NMD_transcript_variant|MODIFIER|BCL2L13|ENSG00000099968|Transcript|ENST00000498133|nonsense_mediated_decay||5/5|ENST00000498133.1:c.*206+6984A>G|||||||rs2535712|1||1||SNV|HGNC|17164|||||ENSP00000436321||F2Z2C3|UPI000155D5B6||Ensembl|A|A||||||||0.8582|0.907|0.8516|0.9375|0.8121|0.7628||||||||||||0.9375|EAS||||||||||||,G|intron_variant|MODIFIER|BCL2L13|ENSG00000099968|Transcript|ENST00000538149|protein_coding||3/3|ENST00000538149.1:c.228+6984A>G|||||||rs2535712|1||1||SNV|HGNC|17164|||||ENSP00000441344||B7Z238|UPI0001914B19||Ensembl|A|A||||||||0.8582|0.907|0.8516|0.9375|0.8121|0.7628||||||||||||0.9375|EAS||||||||||||,G|intron_variant|MODIFIER|BCL2L13|ENSG00000099968|Transcript|ENST00000543133|protein_coding||5/5|ENST00000543133.1:c.114+6984A>G|||||||rs2535712|1||1||SNV|HGNC|17164||||CCDS59448.1|ENSP00000437667|Q9BXK5||UPI00001A3E35||Ensembl|A|A||||||||0.8582|0.907|0.8516|0.9375|0.8121|0.7628||||||||||||0.9375|EAS||||||||||||,G|intron_variant|MODIFIER|BCL2L13|23786|Transcript|NM_001270726.1|protein_coding||5/5|NM_001270726.1:c.672+6984A>G|||||||rs2535712|1||1||SNV|EntrezGene|17164|||||NP_001257655.1|||||RefSeq|A|A||||||||0.8582|0.907|0.8516|0.9375|0.8121|0.7628||||||||||||0.9375|EAS||||||||||||,G|intron_variant|MODIFIER|BCL2L13|23786|Transcript|NM_001270727.1|protein_coding||4/4|NM_001270727.1:c.528+13160A>G|||||||rs2535712|1||1||SNV|EntrezGene|17164|||||NP_001257656.1|||||RefSeq|A|A||||||||0.8582|0.907|0.8516|0.9375|0.8121|0.7628||||||||||||0.9375|EAS||||||||||||,G|intron_variant|MODIFIER|BCL2L13|23786|Transcript|NM_001270728.1|protein_coding||3/3|NM_001270728.1:c.265+6984A>G|||||||rs2535712|1||1||SNV|EntrezGene|17164|||||NP_001257657.1|||||RefSeq|A|A||||||||0.8582|0.907|0.8516|0.9375|0.8121|0.7628||||||||||||0.9375|EAS||||||||||||,G|intron_variant|MODIFIER|BCL2L13|23786|Transcript|NM_001270729.1|protein_coding||5/5|NM_001270729.1:c.114+6984A>G|||||||rs2535712|1||1||SNV|EntrezGene|17164|||||NP_001257658.1|||||RefSeq|A|A||||||||0.8582|0.907|0.8516|0.9375|0.8121|0.7628||||||||||||0.9375|EAS||||||||||||,G|intron_variant|MODIFIER|BCL2L13|23786|Transcript|NM_001270730.1|protein_coding||4/4|NM_001270730.1:c.114+6984A>G|||||||rs2535712|1||1||SNV|EntrezGene|17164|||||NP_001257659.1|||||RefSeq|A|A||||||||0.8582|0.907|0.8516|0.9375|0.8121|0.7628||||||||||||0.9375|EAS||||||||||||,G|intron_variant|MODIFIER|BCL2L13|23786|Transcript|NM_001270731.1|protein_coding||5/5|NM_001270731.1:c.114+6984A>G|||||||rs2535712|1||1||SNV|EntrezGene|17164|||||NP_001257660.1|||||RefSeq|A|A||||||||0.8582|0.907|0.8516|0.9375|0.8121|0.7628||||||||||||0.9375|EAS||||||||||||,G|intron_variant|MODIFIER|BCL2L13|23786|Transcript|NM_001270732.1|protein_coding||4/4|NM_001270732.1:c.373+6984A>G|||||||rs2535712|1||1||SNV|EntrezGene|17164|||||NP_001257661.1|||||RefSeq|A|A||||||||0.8582|0.907|0.8516|0.9375|0.8121|0.7628||||||||||||0.9375|EAS||||||||||||,G|intron_variant|MODIFIER|BCL2L13|23786|Transcript|NM_001270733.1|protein_coding||1/1|NM_001270733.1:c.-241+2545A>G|||||||rs2535712|1||1||SNV|EntrezGene|17164|||||NP_001257662.1|||||RefSeq|A|A||||||||0.8582|0.907|0.8516|0.9375|0.8121|0.7628||||||||||||0.9375|EAS||||||||||||,G|intron_variant|MODIFIER|BCL2L13|23786|Transcript|NM_001270734.1|protein_coding||4/4|NM_001270734.1:c.387-17307A>G|||||||rs2535712|1||1||SNV|EntrezGene|17164|||||NP_001257663.1|||||RefSeq|A|A||||||||0.8582|0.907|0.8516|0.9375|0.8121|0.7628||||||||||||0.9375|EAS||||||||||||,G|intron_variant|MODIFIER|BCL2L13|23786|Transcript|NM_001270735.1|protein_coding||3/3|NM_001270735.1:c.230-17307A>G|||||||rs2535712|1||1||SNV|EntrezGene|17164|||||NP_001257664.1|||||RefSeq|A|A||||||||0.8582|0.907|0.8516|0.9375|0.8121|0.7628||||||||||||0.9375|EAS||||||||||||,G|intron_variant|MODIFIER|BCL2L13|23786|Transcript|NM_015367.3|protein_coding||6/6|NM_015367.3:c.600+6984A>G|||||||rs2535712|1||1||SNV|EntrezGene|17164|||||NP_056182.2|||||RefSeq|A|A||||||||0.8582|0.907|0.8516|0.9375|0.8121|0.7628||||||||||||0.9375|EAS||||||||||||,G|intron_variant&non_coding_transcript_variant|MODIFIER|BCL2L13|23786|Transcript|NR_073068.1|misc_RNA||4/4|NR_073068.1:n.552-17307A>G|||||||rs2535712|1||1||SNV|EntrezGene|17164||||||||||RefSeq|A|A||||||||0.8582|0.907|0.8516|0.9375|0.8121|0.7628||||||||||||0.9375|EAS||||||||||||,G|intron_variant&non_coding_transcript_variant|MODIFIER|BCL2L13|23786|Transcript|NR_073069.1|misc_RNA||4/4|NR_073069.1:n.535-17307A>G|||||||rs2535712|1||1||SNV|EntrezGene|17164||||||||||RefSeq|A|A||||||||0.8582|0.907|0.8516|0.9375|0.8121|0.7628||||||||||||0.9375|EAS||||||||||||,G|intron_variant|MODIFIER|BCL2L13|23786|Transcript|XM_005261231.1|protein_coding||6/6|XM_005261231.1:c.672+6984A>G|||||||rs2535712|1||1||SNV|EntrezGene|17164|YES||||XP_005261288.1|||||RefSeq|A|A||||||||0.8582|0.907|0.8516|0.9375|0.8121|0.7628||||||||||||0.9375|EAS||||||||||||,G|intron_variant|MODIFIER|BCL2L13|23786|Transcript|XM_005261233.1|protein_coding||5/5|XM_005261233.1:c.373+6984A>G|||||||rs2535712|1||1||SNV|EntrezGene|17164|||||XP_005261290.1|||||RefSeq|A|A||||||||0.8582|0.907|0.8516|0.9375|0.8121|0.7628||||||||||||0.9375|EAS|||||||||||| +22 18193560 22:31532 A G 181696 PASS AC=529;AF=0.882;AN=600;BaseQRankSum=-0.965;ClippingRankSum=0.107;DP=7200;FS=0;GQ_MEAN=105.35;GQ_STDDEV=81.44;HW=9.4;InbreedingCoeff=-0.1017;MLEAC=530;MLEAF=0.883;MQ=60;MQ0=0;MQRankSum=-0.047;NCC=0;POSITIVE_TRAIN_SITE;QD=26.27;ReadPosRankSum=0.35;SOR=0.737;VQSLOD=3.52;culprit=FS;CSQ=G|intron_variant|MODIFIER|BCL2L13|ENSG00000099968|Transcript|ENST00000317582|protein_coding||6/6|ENST00000317582.5:c.600+8408A>G|||||||rs4819462|1||1||SNV|HGNC|17164|YES|||CCDS13746.1|ENSP00000318883|Q9BXK5|B2RB43|UPI000004F301||Ensembl|A|A|||||||||0.9092|0.8501|0.9375|0.8121|0.7628||||||||||||0.9375|EAS||||||||||||,G|intron_variant|MODIFIER|BCL2L13|ENSG00000099968|Transcript|ENST00000337612|protein_coding||4/4|ENST00000337612.5:c.114+8408A>G|||||||rs4819462|1||1||SNV|HGNC|17164||||CCDS59448.1|ENSP00000338932|Q9BXK5||UPI00001A3E35||Ensembl|A|A|||||||||0.9092|0.8501|0.9375|0.8121|0.7628||||||||||||0.9375|EAS||||||||||||,G|intron_variant|MODIFIER|BCL2L13|ENSG00000099968|Transcript|ENST00000355028|protein_coding||4/4|ENST00000355028.3:c.387-15883A>G|||||||rs4819462|1||1||SNV|HGNC|17164||||CCDS59447.1|ENSP00000347133||E9PDD6|UPI0000246DFE||Ensembl|A|A|||||||||0.9092|0.8501|0.9375|0.8121|0.7628||||||||||||0.9375|EAS||||||||||||,G|intron_variant&NMD_transcript_variant|MODIFIER|BCL2L13|ENSG00000099968|Transcript|ENST00000399777|nonsense_mediated_decay||2/2|ENST00000399777.1:c.*98+8408A>G|||||||rs4819462|1||1|cds_start_NF|SNV|HGNC|17164|||||ENSP00000382677|||UPI0001F77C70||Ensembl|A|A|||||||||0.9092|0.8501|0.9375|0.8121|0.7628||||||||||||0.9375|EAS||||||||||||,G|intron_variant|MODIFIER|BCL2L13|ENSG00000099968|Transcript|ENST00000418951|protein_coding||4/4|ENST00000418951.2:c.*170-15883A>G|||||||rs4819462|1||1||SNV|HGNC|17164|||||ENSP00000410019||Q8IZP5|UPI00000740D0||Ensembl|A|A|||||||||0.9092|0.8501|0.9375|0.8121|0.7628||||||||||||0.9375|EAS||||||||||||,G|intron_variant&non_coding_transcript_variant|MODIFIER|BCL2L13|ENSG00000099968|Transcript|ENST00000485631|processed_transcript||1/1|ENST00000485631.1:n.116+3969A>G|||||||rs4819462|1||1||SNV|HGNC|17164||||||||||Ensembl|A|A|||||||||0.9092|0.8501|0.9375|0.8121|0.7628||||||||||||0.9375|EAS||||||||||||,G|intron_variant&NMD_transcript_variant|MODIFIER|BCL2L13|ENSG00000099968|Transcript|ENST00000498133|nonsense_mediated_decay||5/5|ENST00000498133.1:c.*206+8408A>G|||||||rs4819462|1||1||SNV|HGNC|17164|||||ENSP00000436321||F2Z2C3|UPI000155D5B6||Ensembl|A|A|||||||||0.9092|0.8501|0.9375|0.8121|0.7628||||||||||||0.9375|EAS||||||||||||,G|intron_variant|MODIFIER|BCL2L13|ENSG00000099968|Transcript|ENST00000538149|protein_coding||3/3|ENST00000538149.1:c.228+8408A>G|||||||rs4819462|1||1||SNV|HGNC|17164|||||ENSP00000441344||B7Z238|UPI0001914B19||Ensembl|A|A|||||||||0.9092|0.8501|0.9375|0.8121|0.7628||||||||||||0.9375|EAS||||||||||||,G|intron_variant|MODIFIER|BCL2L13|ENSG00000099968|Transcript|ENST00000543133|protein_coding||5/5|ENST00000543133.1:c.114+8408A>G|||||||rs4819462|1||1||SNV|HGNC|17164||||CCDS59448.1|ENSP00000437667|Q9BXK5||UPI00001A3E35||Ensembl|A|A|||||||||0.9092|0.8501|0.9375|0.8121|0.7628||||||||||||0.9375|EAS||||||||||||,G|intron_variant|MODIFIER|BCL2L13|23786|Transcript|NM_001270726.1|protein_coding||5/5|NM_001270726.1:c.672+8408A>G|||||||rs4819462|1||1||SNV|EntrezGene|17164|||||NP_001257655.1|||||RefSeq|A|A|||||||||0.9092|0.8501|0.9375|0.8121|0.7628||||||||||||0.9375|EAS||||||||||||,G|intron_variant|MODIFIER|BCL2L13|23786|Transcript|NM_001270727.1|protein_coding||4/4|NM_001270727.1:c.528+14584A>G|||||||rs4819462|1||1||SNV|EntrezGene|17164|||||NP_001257656.1|||||RefSeq|A|A|||||||||0.9092|0.8501|0.9375|0.8121|0.7628||||||||||||0.9375|EAS||||||||||||,G|intron_variant|MODIFIER|BCL2L13|23786|Transcript|NM_001270728.1|protein_coding||3/3|NM_001270728.1:c.265+8408A>G|||||||rs4819462|1||1||SNV|EntrezGene|17164|||||NP_001257657.1|||||RefSeq|A|A|||||||||0.9092|0.8501|0.9375|0.8121|0.7628||||||||||||0.9375|EAS||||||||||||,G|intron_variant|MODIFIER|BCL2L13|23786|Transcript|NM_001270729.1|protein_coding||5/5|NM_001270729.1:c.114+8408A>G|||||||rs4819462|1||1||SNV|EntrezGene|17164|||||NP_001257658.1|||||RefSeq|A|A|||||||||0.9092|0.8501|0.9375|0.8121|0.7628||||||||||||0.9375|EAS||||||||||||,G|intron_variant|MODIFIER|BCL2L13|23786|Transcript|NM_001270730.1|protein_coding||4/4|NM_001270730.1:c.114+8408A>G|||||||rs4819462|1||1||SNV|EntrezGene|17164|||||NP_001257659.1|||||RefSeq|A|A|||||||||0.9092|0.8501|0.9375|0.8121|0.7628||||||||||||0.9375|EAS||||||||||||,G|intron_variant|MODIFIER|BCL2L13|23786|Transcript|NM_001270731.1|protein_coding||5/5|NM_001270731.1:c.114+8408A>G|||||||rs4819462|1||1||SNV|EntrezGene|17164|||||NP_001257660.1|||||RefSeq|A|A|||||||||0.9092|0.8501|0.9375|0.8121|0.7628||||||||||||0.9375|EAS||||||||||||,G|intron_variant|MODIFIER|BCL2L13|23786|Transcript|NM_001270732.1|protein_coding||4/4|NM_001270732.1:c.373+8408A>G|||||||rs4819462|1||1||SNV|EntrezGene|17164|||||NP_001257661.1|||||RefSeq|A|A|||||||||0.9092|0.8501|0.9375|0.8121|0.7628||||||||||||0.9375|EAS||||||||||||,G|intron_variant|MODIFIER|BCL2L13|23786|Transcript|NM_001270733.1|protein_coding||1/1|NM_001270733.1:c.-241+3969A>G|||||||rs4819462|1||1||SNV|EntrezGene|17164|||||NP_001257662.1|||||RefSeq|A|A|||||||||0.9092|0.8501|0.9375|0.8121|0.7628||||||||||||0.9375|EAS||||||||||||,G|intron_variant|MODIFIER|BCL2L13|23786|Transcript|NM_001270734.1|protein_coding||4/4|NM_001270734.1:c.387-15883A>G|||||||rs4819462|1||1||SNV|EntrezGene|17164|||||NP_001257663.1|||||RefSeq|A|A|||||||||0.9092|0.8501|0.9375|0.8121|0.7628||||||||||||0.9375|EAS||||||||||||,G|intron_variant|MODIFIER|BCL2L13|23786|Transcript|NM_001270735.1|protein_coding||3/3|NM_001270735.1:c.230-15883A>G|||||||rs4819462|1||1||SNV|EntrezGene|17164|||||NP_001257664.1|||||RefSeq|A|A|||||||||0.9092|0.8501|0.9375|0.8121|0.7628||||||||||||0.9375|EAS||||||||||||,G|intron_variant|MODIFIER|BCL2L13|23786|Transcript|NM_015367.3|protein_coding||6/6|NM_015367.3:c.600+8408A>G|||||||rs4819462|1||1||SNV|EntrezGene|17164|||||NP_056182.2|||||RefSeq|A|A|||||||||0.9092|0.8501|0.9375|0.8121|0.7628||||||||||||0.9375|EAS||||||||||||,G|intron_variant&non_coding_transcript_variant|MODIFIER|BCL2L13|23786|Transcript|NR_073068.1|misc_RNA||4/4|NR_073068.1:n.552-15883A>G|||||||rs4819462|1||1||SNV|EntrezGene|17164||||||||||RefSeq|A|A|||||||||0.9092|0.8501|0.9375|0.8121|0.7628||||||||||||0.9375|EAS||||||||||||,G|intron_variant&non_coding_transcript_variant|MODIFIER|BCL2L13|23786|Transcript|NR_073069.1|misc_RNA||4/4|NR_073069.1:n.535-15883A>G|||||||rs4819462|1||1||SNV|EntrezGene|17164||||||||||RefSeq|A|A|||||||||0.9092|0.8501|0.9375|0.8121|0.7628||||||||||||0.9375|EAS||||||||||||,G|intron_variant|MODIFIER|BCL2L13|23786|Transcript|XM_005261231.1|protein_coding||6/6|XM_005261231.1:c.672+8408A>G|||||||rs4819462|1||1||SNV|EntrezGene|17164|YES||||XP_005261288.1|||||RefSeq|A|A|||||||||0.9092|0.8501|0.9375|0.8121|0.7628||||||||||||0.9375|EAS||||||||||||,G|intron_variant|MODIFIER|BCL2L13|23786|Transcript|XM_005261233.1|protein_coding||5/5|XM_005261233.1:c.373+8408A>G|||||||rs4819462|1||1||SNV|EntrezGene|17164|||||XP_005261290.1|||||RefSeq|A|A|||||||||0.9092|0.8501|0.9375|0.8121|0.7628||||||||||||0.9375|EAS|||||||||||| +22 18197172 22:31561 G C 192554 PASS AC=522;AF=0.87;AN=600;BaseQRankSum=-1.623;ClippingRankSum=-0.075;DP=7689;FS=0;GQ_MEAN=115.53;GQ_STDDEV=96.12;HW=7.4;InbreedingCoeff=-0.1035;MLEAC=523;MLEAF=0.872;MQ=60;MQ0=0;MQRankSum=0.026;NCC=0;POSITIVE_TRAIN_SITE;QD=25.84;ReadPosRankSum=0.416;SOR=0.621;VQSLOD=3.47;culprit=FS;CSQ=C|intron_variant|MODIFIER|BCL2L13|ENSG00000099968|Transcript|ENST00000317582|protein_coding||6/6|ENST00000317582.5:c.600+12020G>C|||||||rs5992098|1||1||SNV|HGNC|17164|YES|||CCDS13746.1|ENSP00000318883|Q9BXK5|B2RB43|UPI000004F301||Ensembl|G|G|||||||||0.9092|0.8516|0.9375|0.8121|0.7628||||||||||||0.9375|EAS||||||||||||,C|intron_variant|MODIFIER|BCL2L13|ENSG00000099968|Transcript|ENST00000337612|protein_coding||4/4|ENST00000337612.5:c.114+12020G>C|||||||rs5992098|1||1||SNV|HGNC|17164||||CCDS59448.1|ENSP00000338932|Q9BXK5||UPI00001A3E35||Ensembl|G|G|||||||||0.9092|0.8516|0.9375|0.8121|0.7628||||||||||||0.9375|EAS||||||||||||,C|intron_variant|MODIFIER|BCL2L13|ENSG00000099968|Transcript|ENST00000355028|protein_coding||4/4|ENST00000355028.3:c.387-12271G>C|||||||rs5992098|1||1||SNV|HGNC|17164||||CCDS59447.1|ENSP00000347133||E9PDD6|UPI0000246DFE||Ensembl|G|G|||||||||0.9092|0.8516|0.9375|0.8121|0.7628||||||||||||0.9375|EAS||||||||||||,C|intron_variant&NMD_transcript_variant|MODIFIER|BCL2L13|ENSG00000099968|Transcript|ENST00000399777|nonsense_mediated_decay||2/2|ENST00000399777.1:c.*98+12020G>C|||||||rs5992098|1||1|cds_start_NF|SNV|HGNC|17164|||||ENSP00000382677|||UPI0001F77C70||Ensembl|G|G|||||||||0.9092|0.8516|0.9375|0.8121|0.7628||||||||||||0.9375|EAS||||||||||||,C|intron_variant|MODIFIER|BCL2L13|ENSG00000099968|Transcript|ENST00000418951|protein_coding||4/4|ENST00000418951.2:c.*170-12271G>C|||||||rs5992098|1||1||SNV|HGNC|17164|||||ENSP00000410019||Q8IZP5|UPI00000740D0||Ensembl|G|G|||||||||0.9092|0.8516|0.9375|0.8121|0.7628||||||||||||0.9375|EAS||||||||||||,C|intron_variant&non_coding_transcript_variant|MODIFIER|BCL2L13|ENSG00000099968|Transcript|ENST00000485631|processed_transcript||1/1|ENST00000485631.1:n.116+7581G>C|||||||rs5992098|1||1||SNV|HGNC|17164||||||||||Ensembl|G|G|||||||||0.9092|0.8516|0.9375|0.8121|0.7628||||||||||||0.9375|EAS||||||||||||,C|intron_variant&NMD_transcript_variant|MODIFIER|BCL2L13|ENSG00000099968|Transcript|ENST00000498133|nonsense_mediated_decay||5/5|ENST00000498133.1:c.*206+12020G>C|||||||rs5992098|1||1||SNV|HGNC|17164|||||ENSP00000436321||F2Z2C3|UPI000155D5B6||Ensembl|G|G|||||||||0.9092|0.8516|0.9375|0.8121|0.7628||||||||||||0.9375|EAS||||||||||||,C|intron_variant|MODIFIER|BCL2L13|ENSG00000099968|Transcript|ENST00000538149|protein_coding||3/3|ENST00000538149.1:c.228+12020G>C|||||||rs5992098|1||1||SNV|HGNC|17164|||||ENSP00000441344||B7Z238|UPI0001914B19||Ensembl|G|G|||||||||0.9092|0.8516|0.9375|0.8121|0.7628||||||||||||0.9375|EAS||||||||||||,C|intron_variant|MODIFIER|BCL2L13|ENSG00000099968|Transcript|ENST00000543133|protein_coding||5/5|ENST00000543133.1:c.114+12020G>C|||||||rs5992098|1||1||SNV|HGNC|17164||||CCDS59448.1|ENSP00000437667|Q9BXK5||UPI00001A3E35||Ensembl|G|G|||||||||0.9092|0.8516|0.9375|0.8121|0.7628||||||||||||0.9375|EAS||||||||||||,C|intron_variant|MODIFIER|BCL2L13|23786|Transcript|NM_001270726.1|protein_coding||5/5|NM_001270726.1:c.672+12020G>C|||||||rs5992098|1||1||SNV|EntrezGene|17164|||||NP_001257655.1|||||RefSeq|G|G|||||||||0.9092|0.8516|0.9375|0.8121|0.7628||||||||||||0.9375|EAS||||||||||||,C|intron_variant|MODIFIER|BCL2L13|23786|Transcript|NM_001270727.1|protein_coding||4/4|NM_001270727.1:c.529-12271G>C|||||||rs5992098|1||1||SNV|EntrezGene|17164|||||NP_001257656.1|||||RefSeq|G|G|||||||||0.9092|0.8516|0.9375|0.8121|0.7628||||||||||||0.9375|EAS||||||||||||,C|intron_variant|MODIFIER|BCL2L13|23786|Transcript|NM_001270728.1|protein_coding||3/3|NM_001270728.1:c.265+12020G>C|||||||rs5992098|1||1||SNV|EntrezGene|17164|||||NP_001257657.1|||||RefSeq|G|G|||||||||0.9092|0.8516|0.9375|0.8121|0.7628||||||||||||0.9375|EAS||||||||||||,C|intron_variant|MODIFIER|BCL2L13|23786|Transcript|NM_001270729.1|protein_coding||5/5|NM_001270729.1:c.114+12020G>C|||||||rs5992098|1||1||SNV|EntrezGene|17164|||||NP_001257658.1|||||RefSeq|G|G|||||||||0.9092|0.8516|0.9375|0.8121|0.7628||||||||||||0.9375|EAS||||||||||||,C|intron_variant|MODIFIER|BCL2L13|23786|Transcript|NM_001270730.1|protein_coding||4/4|NM_001270730.1:c.114+12020G>C|||||||rs5992098|1||1||SNV|EntrezGene|17164|||||NP_001257659.1|||||RefSeq|G|G|||||||||0.9092|0.8516|0.9375|0.8121|0.7628||||||||||||0.9375|EAS||||||||||||,C|intron_variant|MODIFIER|BCL2L13|23786|Transcript|NM_001270731.1|protein_coding||5/5|NM_001270731.1:c.114+12020G>C|||||||rs5992098|1||1||SNV|EntrezGene|17164|||||NP_001257660.1|||||RefSeq|G|G|||||||||0.9092|0.8516|0.9375|0.8121|0.7628||||||||||||0.9375|EAS||||||||||||,C|intron_variant|MODIFIER|BCL2L13|23786|Transcript|NM_001270732.1|protein_coding||4/4|NM_001270732.1:c.373+12020G>C|||||||rs5992098|1||1||SNV|EntrezGene|17164|||||NP_001257661.1|||||RefSeq|G|G|||||||||0.9092|0.8516|0.9375|0.8121|0.7628||||||||||||0.9375|EAS||||||||||||,C|intron_variant|MODIFIER|BCL2L13|23786|Transcript|NM_001270733.1|protein_coding||1/1|NM_001270733.1:c.-241+7581G>C|||||||rs5992098|1||1||SNV|EntrezGene|17164|||||NP_001257662.1|||||RefSeq|G|G|||||||||0.9092|0.8516|0.9375|0.8121|0.7628||||||||||||0.9375|EAS||||||||||||,C|intron_variant|MODIFIER|BCL2L13|23786|Transcript|NM_001270734.1|protein_coding||4/4|NM_001270734.1:c.387-12271G>C|||||||rs5992098|1||1||SNV|EntrezGene|17164|||||NP_001257663.1|||||RefSeq|G|G|||||||||0.9092|0.8516|0.9375|0.8121|0.7628||||||||||||0.9375|EAS||||||||||||,C|intron_variant|MODIFIER|BCL2L13|23786|Transcript|NM_001270735.1|protein_coding||3/3|NM_001270735.1:c.230-12271G>C|||||||rs5992098|1||1||SNV|EntrezGene|17164|||||NP_001257664.1|||||RefSeq|G|G|||||||||0.9092|0.8516|0.9375|0.8121|0.7628||||||||||||0.9375|EAS||||||||||||,C|intron_variant|MODIFIER|BCL2L13|23786|Transcript|NM_015367.3|protein_coding||6/6|NM_015367.3:c.600+12020G>C|||||||rs5992098|1||1||SNV|EntrezGene|17164|||||NP_056182.2|||||RefSeq|G|G|||||||||0.9092|0.8516|0.9375|0.8121|0.7628||||||||||||0.9375|EAS||||||||||||,C|intron_variant&non_coding_transcript_variant|MODIFIER|BCL2L13|23786|Transcript|NR_073068.1|misc_RNA||4/4|NR_073068.1:n.552-12271G>C|||||||rs5992098|1||1||SNV|EntrezGene|17164||||||||||RefSeq|G|G|||||||||0.9092|0.8516|0.9375|0.8121|0.7628||||||||||||0.9375|EAS||||||||||||,C|intron_variant&non_coding_transcript_variant|MODIFIER|BCL2L13|23786|Transcript|NR_073069.1|misc_RNA||4/4|NR_073069.1:n.535-12271G>C|||||||rs5992098|1||1||SNV|EntrezGene|17164||||||||||RefSeq|G|G|||||||||0.9092|0.8516|0.9375|0.8121|0.7628||||||||||||0.9375|EAS||||||||||||,C|intron_variant|MODIFIER|BCL2L13|23786|Transcript|XM_005261231.1|protein_coding||6/6|XM_005261231.1:c.672+12020G>C|||||||rs5992098|1||1||SNV|EntrezGene|17164|YES||||XP_005261288.1|||||RefSeq|G|G|||||||||0.9092|0.8516|0.9375|0.8121|0.7628||||||||||||0.9375|EAS||||||||||||,C|intron_variant|MODIFIER|BCL2L13|23786|Transcript|XM_005261233.1|protein_coding||5/5|XM_005261233.1:c.373+12020G>C|||||||rs5992098|1||1||SNV|EntrezGene|17164|||||XP_005261290.1|||||RefSeq|G|G|||||||||0.9092|0.8516|0.9375|0.8121|0.7628||||||||||||0.9375|EAS|||||||||||| +22 18198327 22:31607 C G 244937 PASS AC=524;AF=0.873;AN=600;BaseQRankSum=0.217;ClippingRankSum=0.168;DP=9590;FS=0.858;GQ_MEAN=144.45;GQ_STDDEV=106.27;HW=12;InbreedingCoeff=-0.1149;MLEAC=524;MLEAF=0.873;MQ=60;MQ0=0;MQRankSum=-0.029;NCC=0;POSITIVE_TRAIN_SITE;QD=26.7;ReadPosRankSum=0.491;SOR=0.644;VQSLOD=4.19;culprit=QD;CSQ=G|intron_variant|MODIFIER|BCL2L13|ENSG00000099968|Transcript|ENST00000317582|protein_coding||6/6|ENST00000317582.5:c.601-11116C>G|||||||rs2109659|1||1||SNV|HGNC|17164|YES|||CCDS13746.1|ENSP00000318883|Q9BXK5|B2RB43|UPI000004F301||Ensembl|C|C||||||||0.8648|0.9289|0.853|0.9375|0.8151|0.7628||||||||||||0.9375|EAS||||||||||||,G|intron_variant|MODIFIER|BCL2L13|ENSG00000099968|Transcript|ENST00000337612|protein_coding||4/4|ENST00000337612.5:c.115-11116C>G|||||||rs2109659|1||1||SNV|HGNC|17164||||CCDS59448.1|ENSP00000338932|Q9BXK5||UPI00001A3E35||Ensembl|C|C||||||||0.8648|0.9289|0.853|0.9375|0.8151|0.7628||||||||||||0.9375|EAS||||||||||||,G|intron_variant|MODIFIER|BCL2L13|ENSG00000099968|Transcript|ENST00000355028|protein_coding||4/4|ENST00000355028.3:c.387-11116C>G|||||||rs2109659|1||1||SNV|HGNC|17164||||CCDS59447.1|ENSP00000347133||E9PDD6|UPI0000246DFE||Ensembl|C|C||||||||0.8648|0.9289|0.853|0.9375|0.8151|0.7628||||||||||||0.9375|EAS||||||||||||,G|intron_variant&NMD_transcript_variant|MODIFIER|BCL2L13|ENSG00000099968|Transcript|ENST00000399777|nonsense_mediated_decay||2/2|ENST00000399777.1:c.*99-11116C>G|||||||rs2109659|1||1|cds_start_NF|SNV|HGNC|17164|||||ENSP00000382677|||UPI0001F77C70||Ensembl|C|C||||||||0.8648|0.9289|0.853|0.9375|0.8151|0.7628||||||||||||0.9375|EAS||||||||||||,G|intron_variant|MODIFIER|BCL2L13|ENSG00000099968|Transcript|ENST00000418951|protein_coding||4/4|ENST00000418951.2:c.*170-11116C>G|||||||rs2109659|1||1||SNV|HGNC|17164|||||ENSP00000410019||Q8IZP5|UPI00000740D0||Ensembl|C|C||||||||0.8648|0.9289|0.853|0.9375|0.8151|0.7628||||||||||||0.9375|EAS||||||||||||,G|intron_variant&non_coding_transcript_variant|MODIFIER|BCL2L13|ENSG00000099968|Transcript|ENST00000485631|processed_transcript||1/1|ENST00000485631.1:n.116+8736C>G|||||||rs2109659|1||1||SNV|HGNC|17164||||||||||Ensembl|C|C||||||||0.8648|0.9289|0.853|0.9375|0.8151|0.7628||||||||||||0.9375|EAS||||||||||||,G|intron_variant&NMD_transcript_variant|MODIFIER|BCL2L13|ENSG00000099968|Transcript|ENST00000498133|nonsense_mediated_decay||5/5|ENST00000498133.1:c.*207-11116C>G|||||||rs2109659|1||1||SNV|HGNC|17164|||||ENSP00000436321||F2Z2C3|UPI000155D5B6||Ensembl|C|C||||||||0.8648|0.9289|0.853|0.9375|0.8151|0.7628||||||||||||0.9375|EAS||||||||||||,G|intron_variant|MODIFIER|BCL2L13|ENSG00000099968|Transcript|ENST00000538149|protein_coding||3/3|ENST00000538149.1:c.229-11116C>G|||||||rs2109659|1||1||SNV|HGNC|17164|||||ENSP00000441344||B7Z238|UPI0001914B19||Ensembl|C|C||||||||0.8648|0.9289|0.853|0.9375|0.8151|0.7628||||||||||||0.9375|EAS||||||||||||,G|intron_variant|MODIFIER|BCL2L13|ENSG00000099968|Transcript|ENST00000543133|protein_coding||5/5|ENST00000543133.1:c.115-11116C>G|||||||rs2109659|1||1||SNV|HGNC|17164||||CCDS59448.1|ENSP00000437667|Q9BXK5||UPI00001A3E35||Ensembl|C|C||||||||0.8648|0.9289|0.853|0.9375|0.8151|0.7628||||||||||||0.9375|EAS||||||||||||,G|intron_variant|MODIFIER|BCL2L13|23786|Transcript|NM_001270726.1|protein_coding||5/5|NM_001270726.1:c.673-11116C>G|||||||rs2109659|1||1||SNV|EntrezGene|17164|||||NP_001257655.1|||||RefSeq|C|C||||||||0.8648|0.9289|0.853|0.9375|0.8151|0.7628||||||||||||0.9375|EAS||||||||||||,G|intron_variant|MODIFIER|BCL2L13|23786|Transcript|NM_001270727.1|protein_coding||4/4|NM_001270727.1:c.529-11116C>G|||||||rs2109659|1||1||SNV|EntrezGene|17164|||||NP_001257656.1|||||RefSeq|C|C||||||||0.8648|0.9289|0.853|0.9375|0.8151|0.7628||||||||||||0.9375|EAS||||||||||||,G|intron_variant|MODIFIER|BCL2L13|23786|Transcript|NM_001270728.1|protein_coding||3/3|NM_001270728.1:c.266-11116C>G|||||||rs2109659|1||1||SNV|EntrezGene|17164|||||NP_001257657.1|||||RefSeq|C|C||||||||0.8648|0.9289|0.853|0.9375|0.8151|0.7628||||||||||||0.9375|EAS||||||||||||,G|intron_variant|MODIFIER|BCL2L13|23786|Transcript|NM_001270729.1|protein_coding||5/5|NM_001270729.1:c.115-11116C>G|||||||rs2109659|1||1||SNV|EntrezGene|17164|||||NP_001257658.1|||||RefSeq|C|C||||||||0.8648|0.9289|0.853|0.9375|0.8151|0.7628||||||||||||0.9375|EAS||||||||||||,G|intron_variant|MODIFIER|BCL2L13|23786|Transcript|NM_001270730.1|protein_coding||4/4|NM_001270730.1:c.115-11116C>G|||||||rs2109659|1||1||SNV|EntrezGene|17164|||||NP_001257659.1|||||RefSeq|C|C||||||||0.8648|0.9289|0.853|0.9375|0.8151|0.7628||||||||||||0.9375|EAS||||||||||||,G|intron_variant|MODIFIER|BCL2L13|23786|Transcript|NM_001270731.1|protein_coding||5/5|NM_001270731.1:c.115-11116C>G|||||||rs2109659|1||1||SNV|EntrezGene|17164|||||NP_001257660.1|||||RefSeq|C|C||||||||0.8648|0.9289|0.853|0.9375|0.8151|0.7628||||||||||||0.9375|EAS||||||||||||,G|intron_variant|MODIFIER|BCL2L13|23786|Transcript|NM_001270732.1|protein_coding||4/4|NM_001270732.1:c.374-11116C>G|||||||rs2109659|1||1||SNV|EntrezGene|17164|||||NP_001257661.1|||||RefSeq|C|C||||||||0.8648|0.9289|0.853|0.9375|0.8151|0.7628||||||||||||0.9375|EAS||||||||||||,G|intron_variant|MODIFIER|BCL2L13|23786|Transcript|NM_001270733.1|protein_coding||1/1|NM_001270733.1:c.-241+8736C>G|||||||rs2109659|1||1||SNV|EntrezGene|17164|||||NP_001257662.1|||||RefSeq|C|C||||||||0.8648|0.9289|0.853|0.9375|0.8151|0.7628||||||||||||0.9375|EAS||||||||||||,G|intron_variant|MODIFIER|BCL2L13|23786|Transcript|NM_001270734.1|protein_coding||4/4|NM_001270734.1:c.387-11116C>G|||||||rs2109659|1||1||SNV|EntrezGene|17164|||||NP_001257663.1|||||RefSeq|C|C||||||||0.8648|0.9289|0.853|0.9375|0.8151|0.7628||||||||||||0.9375|EAS||||||||||||,G|intron_variant|MODIFIER|BCL2L13|23786|Transcript|NM_001270735.1|protein_coding||3/3|NM_001270735.1:c.230-11116C>G|||||||rs2109659|1||1||SNV|EntrezGene|17164|||||NP_001257664.1|||||RefSeq|C|C||||||||0.8648|0.9289|0.853|0.9375|0.8151|0.7628||||||||||||0.9375|EAS||||||||||||,G|intron_variant|MODIFIER|BCL2L13|23786|Transcript|NM_015367.3|protein_coding||6/6|NM_015367.3:c.601-11116C>G|||||||rs2109659|1||1||SNV|EntrezGene|17164|||||NP_056182.2|||||RefSeq|C|C||||||||0.8648|0.9289|0.853|0.9375|0.8151|0.7628||||||||||||0.9375|EAS||||||||||||,G|intron_variant&non_coding_transcript_variant|MODIFIER|BCL2L13|23786|Transcript|NR_073068.1|misc_RNA||4/4|NR_073068.1:n.552-11116C>G|||||||rs2109659|1||1||SNV|EntrezGene|17164||||||||||RefSeq|C|C||||||||0.8648|0.9289|0.853|0.9375|0.8151|0.7628||||||||||||0.9375|EAS||||||||||||,G|intron_variant&non_coding_transcript_variant|MODIFIER|BCL2L13|23786|Transcript|NR_073069.1|misc_RNA||4/4|NR_073069.1:n.535-11116C>G|||||||rs2109659|1||1||SNV|EntrezGene|17164||||||||||RefSeq|C|C||||||||0.8648|0.9289|0.853|0.9375|0.8151|0.7628||||||||||||0.9375|EAS||||||||||||,G|intron_variant|MODIFIER|BCL2L13|23786|Transcript|XM_005261231.1|protein_coding||6/6|XM_005261231.1:c.673-11116C>G|||||||rs2109659|1||1||SNV|EntrezGene|17164|YES||||XP_005261288.1|||||RefSeq|C|C||||||||0.8648|0.9289|0.853|0.9375|0.8151|0.7628||||||||||||0.9375|EAS||||||||||||,G|intron_variant|MODIFIER|BCL2L13|23786|Transcript|XM_005261233.1|protein_coding||5/5|XM_005261233.1:c.374-11116C>G|||||||rs2109659|1||1||SNV|EntrezGene|17164|||||XP_005261290.1|||||RefSeq|C|C||||||||0.8648|0.9289|0.853|0.9375|0.8151|0.7628||||||||||||0.9375|EAS|||||||||||| +22 18201526 22:31631 G C 264315 PASS AC=524;AF=0.873;AN=600;BaseQRankSum=0.35;ClippingRankSum=-0.161;DP=9775;FS=0;GQ_MEAN=152.14;GQ_STDDEV=114.04;HW=12;InbreedingCoeff=-0.1149;MLEAC=524;MLEAF=0.873;MQ=60;MQ0=0;MQRankSum=0.084;NCC=0;POSITIVE_TRAIN_SITE;QD=27.91;ReadPosRankSum=0.299;SOR=0.745;VQSLOD=6.05;culprit=FS;CSQ=C|intron_variant|MODIFIER|BCL2L13|ENSG00000099968|Transcript|ENST00000317582|protein_coding||6/6|ENST00000317582.5:c.601-7917G>C|||||||rs2587092|1||1||SNV|HGNC|17164|YES|||CCDS13746.1|ENSP00000318883|Q9BXK5|B2RB43|UPI000004F301||Ensembl|G|G|||||||||0.907|0.8516|0.9375|0.8121|0.7638||||||||||||0.9375|EAS||||||||||||,C|intron_variant|MODIFIER|BCL2L13|ENSG00000099968|Transcript|ENST00000337612|protein_coding||4/4|ENST00000337612.5:c.115-7917G>C|||||||rs2587092|1||1||SNV|HGNC|17164||||CCDS59448.1|ENSP00000338932|Q9BXK5||UPI00001A3E35||Ensembl|G|G|||||||||0.907|0.8516|0.9375|0.8121|0.7638||||||||||||0.9375|EAS||||||||||||,C|intron_variant|MODIFIER|BCL2L13|ENSG00000099968|Transcript|ENST00000355028|protein_coding||4/4|ENST00000355028.3:c.387-7917G>C|||||||rs2587092|1||1||SNV|HGNC|17164||||CCDS59447.1|ENSP00000347133||E9PDD6|UPI0000246DFE||Ensembl|G|G|||||||||0.907|0.8516|0.9375|0.8121|0.7638||||||||||||0.9375|EAS||||||||||||,C|intron_variant&NMD_transcript_variant|MODIFIER|BCL2L13|ENSG00000099968|Transcript|ENST00000399777|nonsense_mediated_decay||2/2|ENST00000399777.1:c.*99-7917G>C|||||||rs2587092|1||1|cds_start_NF|SNV|HGNC|17164|||||ENSP00000382677|||UPI0001F77C70||Ensembl|G|G|||||||||0.907|0.8516|0.9375|0.8121|0.7638||||||||||||0.9375|EAS||||||||||||,C|intron_variant|MODIFIER|BCL2L13|ENSG00000099968|Transcript|ENST00000418951|protein_coding||4/4|ENST00000418951.2:c.*170-7917G>C|||||||rs2587092|1||1||SNV|HGNC|17164|||||ENSP00000410019||Q8IZP5|UPI00000740D0||Ensembl|G|G|||||||||0.907|0.8516|0.9375|0.8121|0.7638||||||||||||0.9375|EAS||||||||||||,C|intron_variant&non_coding_transcript_variant|MODIFIER|BCL2L13|ENSG00000099968|Transcript|ENST00000485631|processed_transcript||1/1|ENST00000485631.1:n.117-7917G>C|||||||rs2587092|1||1||SNV|HGNC|17164||||||||||Ensembl|G|G|||||||||0.907|0.8516|0.9375|0.8121|0.7638||||||||||||0.9375|EAS||||||||||||,C|intron_variant&NMD_transcript_variant|MODIFIER|BCL2L13|ENSG00000099968|Transcript|ENST00000498133|nonsense_mediated_decay||5/5|ENST00000498133.1:c.*207-7917G>C|||||||rs2587092|1||1||SNV|HGNC|17164|||||ENSP00000436321||F2Z2C3|UPI000155D5B6||Ensembl|G|G|||||||||0.907|0.8516|0.9375|0.8121|0.7638||||||||||||0.9375|EAS||||||||||||,C|intron_variant|MODIFIER|BCL2L13|ENSG00000099968|Transcript|ENST00000538149|protein_coding||3/3|ENST00000538149.1:c.229-7917G>C|||||||rs2587092|1||1||SNV|HGNC|17164|||||ENSP00000441344||B7Z238|UPI0001914B19||Ensembl|G|G|||||||||0.907|0.8516|0.9375|0.8121|0.7638||||||||||||0.9375|EAS||||||||||||,C|intron_variant|MODIFIER|BCL2L13|ENSG00000099968|Transcript|ENST00000543133|protein_coding||5/5|ENST00000543133.1:c.115-7917G>C|||||||rs2587092|1||1||SNV|HGNC|17164||||CCDS59448.1|ENSP00000437667|Q9BXK5||UPI00001A3E35||Ensembl|G|G|||||||||0.907|0.8516|0.9375|0.8121|0.7638||||||||||||0.9375|EAS||||||||||||,C|intron_variant|MODIFIER|BCL2L13|23786|Transcript|NM_001270726.1|protein_coding||5/5|NM_001270726.1:c.673-7917G>C|||||||rs2587092|1||1||SNV|EntrezGene|17164|||||NP_001257655.1|||||RefSeq|G|G|||||||||0.907|0.8516|0.9375|0.8121|0.7638||||||||||||0.9375|EAS||||||||||||,C|intron_variant|MODIFIER|BCL2L13|23786|Transcript|NM_001270727.1|protein_coding||4/4|NM_001270727.1:c.529-7917G>C|||||||rs2587092|1||1||SNV|EntrezGene|17164|||||NP_001257656.1|||||RefSeq|G|G|||||||||0.907|0.8516|0.9375|0.8121|0.7638||||||||||||0.9375|EAS||||||||||||,C|intron_variant|MODIFIER|BCL2L13|23786|Transcript|NM_001270728.1|protein_coding||3/3|NM_001270728.1:c.266-7917G>C|||||||rs2587092|1||1||SNV|EntrezGene|17164|||||NP_001257657.1|||||RefSeq|G|G|||||||||0.907|0.8516|0.9375|0.8121|0.7638||||||||||||0.9375|EAS||||||||||||,C|intron_variant|MODIFIER|BCL2L13|23786|Transcript|NM_001270729.1|protein_coding||5/5|NM_001270729.1:c.115-7917G>C|||||||rs2587092|1||1||SNV|EntrezGene|17164|||||NP_001257658.1|||||RefSeq|G|G|||||||||0.907|0.8516|0.9375|0.8121|0.7638||||||||||||0.9375|EAS||||||||||||,C|intron_variant|MODIFIER|BCL2L13|23786|Transcript|NM_001270730.1|protein_coding||4/4|NM_001270730.1:c.115-7917G>C|||||||rs2587092|1||1||SNV|EntrezGene|17164|||||NP_001257659.1|||||RefSeq|G|G|||||||||0.907|0.8516|0.9375|0.8121|0.7638||||||||||||0.9375|EAS||||||||||||,C|intron_variant|MODIFIER|BCL2L13|23786|Transcript|NM_001270731.1|protein_coding||5/5|NM_001270731.1:c.115-7917G>C|||||||rs2587092|1||1||SNV|EntrezGene|17164|||||NP_001257660.1|||||RefSeq|G|G|||||||||0.907|0.8516|0.9375|0.8121|0.7638||||||||||||0.9375|EAS||||||||||||,C|intron_variant|MODIFIER|BCL2L13|23786|Transcript|NM_001270732.1|protein_coding||4/4|NM_001270732.1:c.374-7917G>C|||||||rs2587092|1||1||SNV|EntrezGene|17164|||||NP_001257661.1|||||RefSeq|G|G|||||||||0.907|0.8516|0.9375|0.8121|0.7638||||||||||||0.9375|EAS||||||||||||,C|intron_variant|MODIFIER|BCL2L13|23786|Transcript|NM_001270733.1|protein_coding||1/1|NM_001270733.1:c.-240-7917G>C|||||||rs2587092|1||1||SNV|EntrezGene|17164|||||NP_001257662.1|||||RefSeq|G|G|||||||||0.907|0.8516|0.9375|0.8121|0.7638||||||||||||0.9375|EAS||||||||||||,C|intron_variant|MODIFIER|BCL2L13|23786|Transcript|NM_001270734.1|protein_coding||4/4|NM_001270734.1:c.387-7917G>C|||||||rs2587092|1||1||SNV|EntrezGene|17164|||||NP_001257663.1|||||RefSeq|G|G|||||||||0.907|0.8516|0.9375|0.8121|0.7638||||||||||||0.9375|EAS||||||||||||,C|intron_variant|MODIFIER|BCL2L13|23786|Transcript|NM_001270735.1|protein_coding||3/3|NM_001270735.1:c.230-7917G>C|||||||rs2587092|1||1||SNV|EntrezGene|17164|||||NP_001257664.1|||||RefSeq|G|G|||||||||0.907|0.8516|0.9375|0.8121|0.7638||||||||||||0.9375|EAS||||||||||||,C|intron_variant|MODIFIER|BCL2L13|23786|Transcript|NM_015367.3|protein_coding||6/6|NM_015367.3:c.601-7917G>C|||||||rs2587092|1||1||SNV|EntrezGene|17164|||||NP_056182.2|||||RefSeq|G|G|||||||||0.907|0.8516|0.9375|0.8121|0.7638||||||||||||0.9375|EAS||||||||||||,C|intron_variant&non_coding_transcript_variant|MODIFIER|BCL2L13|23786|Transcript|NR_073068.1|misc_RNA||4/4|NR_073068.1:n.552-7917G>C|||||||rs2587092|1||1||SNV|EntrezGene|17164||||||||||RefSeq|G|G|||||||||0.907|0.8516|0.9375|0.8121|0.7638||||||||||||0.9375|EAS||||||||||||,C|intron_variant&non_coding_transcript_variant|MODIFIER|BCL2L13|23786|Transcript|NR_073069.1|misc_RNA||4/4|NR_073069.1:n.535-7917G>C|||||||rs2587092|1||1||SNV|EntrezGene|17164||||||||||RefSeq|G|G|||||||||0.907|0.8516|0.9375|0.8121|0.7638||||||||||||0.9375|EAS||||||||||||,C|intron_variant|MODIFIER|BCL2L13|23786|Transcript|XM_005261231.1|protein_coding||6/6|XM_005261231.1:c.673-7917G>C|||||||rs2587092|1||1||SNV|EntrezGene|17164|YES||||XP_005261288.1|||||RefSeq|G|G|||||||||0.907|0.8516|0.9375|0.8121|0.7638||||||||||||0.9375|EAS||||||||||||,C|intron_variant|MODIFIER|BCL2L13|23786|Transcript|XM_005261233.1|protein_coding||5/5|XM_005261233.1:c.374-7917G>C|||||||rs2587092|1||1||SNV|EntrezGene|17164|||||XP_005261290.1|||||RefSeq|G|G|||||||||0.907|0.8516|0.9375|0.8121|0.7638||||||||||||0.9375|EAS|||||||||||| +22 18202129 22:31644 A G 248026 PASS AC=524;AF=0.873;AN=600;BaseQRankSum=-0.422;ClippingRankSum=-0.022;DP=9481;FS=1.761;GQ_MEAN=141.64;GQ_STDDEV=111.09;HW=12;InbreedingCoeff=-0.1149;MLEAC=524;MLEAF=0.873;MQ=60;MQ0=0;MQRankSum=0.022;NCC=0;POSITIVE_TRAIN_SITE;QD=28.72;ReadPosRankSum=0.345;SOR=0.612;VQSLOD=3.03;culprit=FS;CSQ=G|intron_variant|MODIFIER|BCL2L13|ENSG00000099968|Transcript|ENST00000317582|protein_coding||6/6|ENST00000317582.5:c.601-7314A>G|||||||rs2535676|1||1||SNV|HGNC|17164|YES|||CCDS13746.1|ENSP00000318883|Q9BXK5|B2RB43|UPI000004F301||Ensembl|A|A|||||||||0.9864|0.8545|0.9375|0.8151|0.7638||||||||||||0.9864|AFR||||||||||||,G|intron_variant|MODIFIER|BCL2L13|ENSG00000099968|Transcript|ENST00000337612|protein_coding||4/4|ENST00000337612.5:c.115-7314A>G|||||||rs2535676|1||1||SNV|HGNC|17164||||CCDS59448.1|ENSP00000338932|Q9BXK5||UPI00001A3E35||Ensembl|A|A|||||||||0.9864|0.8545|0.9375|0.8151|0.7638||||||||||||0.9864|AFR||||||||||||,G|intron_variant|MODIFIER|BCL2L13|ENSG00000099968|Transcript|ENST00000355028|protein_coding||4/4|ENST00000355028.3:c.387-7314A>G|||||||rs2535676|1||1||SNV|HGNC|17164||||CCDS59447.1|ENSP00000347133||E9PDD6|UPI0000246DFE||Ensembl|A|A|||||||||0.9864|0.8545|0.9375|0.8151|0.7638||||||||||||0.9864|AFR||||||||||||,G|intron_variant&NMD_transcript_variant|MODIFIER|BCL2L13|ENSG00000099968|Transcript|ENST00000399777|nonsense_mediated_decay||2/2|ENST00000399777.1:c.*99-7314A>G|||||||rs2535676|1||1|cds_start_NF|SNV|HGNC|17164|||||ENSP00000382677|||UPI0001F77C70||Ensembl|A|A|||||||||0.9864|0.8545|0.9375|0.8151|0.7638||||||||||||0.9864|AFR||||||||||||,G|intron_variant|MODIFIER|BCL2L13|ENSG00000099968|Transcript|ENST00000418951|protein_coding||4/4|ENST00000418951.2:c.*170-7314A>G|||||||rs2535676|1||1||SNV|HGNC|17164|||||ENSP00000410019||Q8IZP5|UPI00000740D0||Ensembl|A|A|||||||||0.9864|0.8545|0.9375|0.8151|0.7638||||||||||||0.9864|AFR||||||||||||,G|intron_variant&non_coding_transcript_variant|MODIFIER|BCL2L13|ENSG00000099968|Transcript|ENST00000485631|processed_transcript||1/1|ENST00000485631.1:n.117-7314A>G|||||||rs2535676|1||1||SNV|HGNC|17164||||||||||Ensembl|A|A|||||||||0.9864|0.8545|0.9375|0.8151|0.7638||||||||||||0.9864|AFR||||||||||||,G|intron_variant&NMD_transcript_variant|MODIFIER|BCL2L13|ENSG00000099968|Transcript|ENST00000498133|nonsense_mediated_decay||5/5|ENST00000498133.1:c.*207-7314A>G|||||||rs2535676|1||1||SNV|HGNC|17164|||||ENSP00000436321||F2Z2C3|UPI000155D5B6||Ensembl|A|A|||||||||0.9864|0.8545|0.9375|0.8151|0.7638||||||||||||0.9864|AFR||||||||||||,G|intron_variant|MODIFIER|BCL2L13|ENSG00000099968|Transcript|ENST00000538149|protein_coding||3/3|ENST00000538149.1:c.229-7314A>G|||||||rs2535676|1||1||SNV|HGNC|17164|||||ENSP00000441344||B7Z238|UPI0001914B19||Ensembl|A|A|||||||||0.9864|0.8545|0.9375|0.8151|0.7638||||||||||||0.9864|AFR||||||||||||,G|intron_variant|MODIFIER|BCL2L13|ENSG00000099968|Transcript|ENST00000543133|protein_coding||5/5|ENST00000543133.1:c.115-7314A>G|||||||rs2535676|1||1||SNV|HGNC|17164||||CCDS59448.1|ENSP00000437667|Q9BXK5||UPI00001A3E35||Ensembl|A|A|||||||||0.9864|0.8545|0.9375|0.8151|0.7638||||||||||||0.9864|AFR||||||||||||,G|intron_variant|MODIFIER|BCL2L13|23786|Transcript|NM_001270726.1|protein_coding||5/5|NM_001270726.1:c.673-7314A>G|||||||rs2535676|1||1||SNV|EntrezGene|17164|||||NP_001257655.1|||||RefSeq|A|A|||||||||0.9864|0.8545|0.9375|0.8151|0.7638||||||||||||0.9864|AFR||||||||||||,G|intron_variant|MODIFIER|BCL2L13|23786|Transcript|NM_001270727.1|protein_coding||4/4|NM_001270727.1:c.529-7314A>G|||||||rs2535676|1||1||SNV|EntrezGene|17164|||||NP_001257656.1|||||RefSeq|A|A|||||||||0.9864|0.8545|0.9375|0.8151|0.7638||||||||||||0.9864|AFR||||||||||||,G|intron_variant|MODIFIER|BCL2L13|23786|Transcript|NM_001270728.1|protein_coding||3/3|NM_001270728.1:c.266-7314A>G|||||||rs2535676|1||1||SNV|EntrezGene|17164|||||NP_001257657.1|||||RefSeq|A|A|||||||||0.9864|0.8545|0.9375|0.8151|0.7638||||||||||||0.9864|AFR||||||||||||,G|intron_variant|MODIFIER|BCL2L13|23786|Transcript|NM_001270729.1|protein_coding||5/5|NM_001270729.1:c.115-7314A>G|||||||rs2535676|1||1||SNV|EntrezGene|17164|||||NP_001257658.1|||||RefSeq|A|A|||||||||0.9864|0.8545|0.9375|0.8151|0.7638||||||||||||0.9864|AFR||||||||||||,G|intron_variant|MODIFIER|BCL2L13|23786|Transcript|NM_001270730.1|protein_coding||4/4|NM_001270730.1:c.115-7314A>G|||||||rs2535676|1||1||SNV|EntrezGene|17164|||||NP_001257659.1|||||RefSeq|A|A|||||||||0.9864|0.8545|0.9375|0.8151|0.7638||||||||||||0.9864|AFR||||||||||||,G|intron_variant|MODIFIER|BCL2L13|23786|Transcript|NM_001270731.1|protein_coding||5/5|NM_001270731.1:c.115-7314A>G|||||||rs2535676|1||1||SNV|EntrezGene|17164|||||NP_001257660.1|||||RefSeq|A|A|||||||||0.9864|0.8545|0.9375|0.8151|0.7638||||||||||||0.9864|AFR||||||||||||,G|intron_variant|MODIFIER|BCL2L13|23786|Transcript|NM_001270732.1|protein_coding||4/4|NM_001270732.1:c.374-7314A>G|||||||rs2535676|1||1||SNV|EntrezGene|17164|||||NP_001257661.1|||||RefSeq|A|A|||||||||0.9864|0.8545|0.9375|0.8151|0.7638||||||||||||0.9864|AFR||||||||||||,G|intron_variant|MODIFIER|BCL2L13|23786|Transcript|NM_001270733.1|protein_coding||1/1|NM_001270733.1:c.-240-7314A>G|||||||rs2535676|1||1||SNV|EntrezGene|17164|||||NP_001257662.1|||||RefSeq|A|A|||||||||0.9864|0.8545|0.9375|0.8151|0.7638||||||||||||0.9864|AFR||||||||||||,G|intron_variant|MODIFIER|BCL2L13|23786|Transcript|NM_001270734.1|protein_coding||4/4|NM_001270734.1:c.387-7314A>G|||||||rs2535676|1||1||SNV|EntrezGene|17164|||||NP_001257663.1|||||RefSeq|A|A|||||||||0.9864|0.8545|0.9375|0.8151|0.7638||||||||||||0.9864|AFR||||||||||||,G|intron_variant|MODIFIER|BCL2L13|23786|Transcript|NM_001270735.1|protein_coding||3/3|NM_001270735.1:c.230-7314A>G|||||||rs2535676|1||1||SNV|EntrezGene|17164|||||NP_001257664.1|||||RefSeq|A|A|||||||||0.9864|0.8545|0.9375|0.8151|0.7638||||||||||||0.9864|AFR||||||||||||,G|intron_variant|MODIFIER|BCL2L13|23786|Transcript|NM_015367.3|protein_coding||6/6|NM_015367.3:c.601-7314A>G|||||||rs2535676|1||1||SNV|EntrezGene|17164|||||NP_056182.2|||||RefSeq|A|A|||||||||0.9864|0.8545|0.9375|0.8151|0.7638||||||||||||0.9864|AFR||||||||||||,G|intron_variant&non_coding_transcript_variant|MODIFIER|BCL2L13|23786|Transcript|NR_073068.1|misc_RNA||4/4|NR_073068.1:n.552-7314A>G|||||||rs2535676|1||1||SNV|EntrezGene|17164||||||||||RefSeq|A|A|||||||||0.9864|0.8545|0.9375|0.8151|0.7638||||||||||||0.9864|AFR||||||||||||,G|intron_variant&non_coding_transcript_variant|MODIFIER|BCL2L13|23786|Transcript|NR_073069.1|misc_RNA||4/4|NR_073069.1:n.535-7314A>G|||||||rs2535676|1||1||SNV|EntrezGene|17164||||||||||RefSeq|A|A|||||||||0.9864|0.8545|0.9375|0.8151|0.7638||||||||||||0.9864|AFR||||||||||||,G|intron_variant|MODIFIER|BCL2L13|23786|Transcript|XM_005261231.1|protein_coding||6/6|XM_005261231.1:c.673-7314A>G|||||||rs2535676|1||1||SNV|EntrezGene|17164|YES||||XP_005261288.1|||||RefSeq|A|A|||||||||0.9864|0.8545|0.9375|0.8151|0.7638||||||||||||0.9864|AFR||||||||||||,G|intron_variant|MODIFIER|BCL2L13|23786|Transcript|XM_005261233.1|protein_coding||5/5|XM_005261233.1:c.374-7314A>G|||||||rs2535676|1||1||SNV|EntrezGene|17164|||||XP_005261290.1|||||RefSeq|A|A|||||||||0.9864|0.8545|0.9375|0.8151|0.7638||||||||||||0.9864|AFR|||||||||||| +22 18202207 22:31646 A G 265777 PASS AC=524;AF=0.873;AN=600;BaseQRankSum=0.321;ClippingRankSum=-0.139;DP=11034;FS=0.814;GQ_MEAN=159.7;GQ_STDDEV=119.14;HW=12;InbreedingCoeff=-0.1149;MLEAC=524;MLEAF=0.873;MQ=60;MQ0=0;MQRankSum=-0.116;NCC=0;POSITIVE_TRAIN_SITE;QD=26.43;ReadPosRankSum=0.601;SOR=0.536;VQSLOD=3.05;culprit=QD;CSQ=G|intron_variant|MODIFIER|BCL2L13|ENSG00000099968|Transcript|ENST00000317582|protein_coding||6/6|ENST00000317582.5:c.601-7236A>G|||||||rs2535677|1||1||SNV|HGNC|17164|YES|||CCDS13746.1|ENSP00000318883|Q9BXK5|B2RB43|UPI000004F301||Ensembl|A|A||||||||0.859|0.9092|0.8516|0.9375|0.8121|0.7638||||||||||||0.9375|EAS||||||||||||,G|intron_variant|MODIFIER|BCL2L13|ENSG00000099968|Transcript|ENST00000337612|protein_coding||4/4|ENST00000337612.5:c.115-7236A>G|||||||rs2535677|1||1||SNV|HGNC|17164||||CCDS59448.1|ENSP00000338932|Q9BXK5||UPI00001A3E35||Ensembl|A|A||||||||0.859|0.9092|0.8516|0.9375|0.8121|0.7638||||||||||||0.9375|EAS||||||||||||,G|intron_variant|MODIFIER|BCL2L13|ENSG00000099968|Transcript|ENST00000355028|protein_coding||4/4|ENST00000355028.3:c.387-7236A>G|||||||rs2535677|1||1||SNV|HGNC|17164||||CCDS59447.1|ENSP00000347133||E9PDD6|UPI0000246DFE||Ensembl|A|A||||||||0.859|0.9092|0.8516|0.9375|0.8121|0.7638||||||||||||0.9375|EAS||||||||||||,G|intron_variant&NMD_transcript_variant|MODIFIER|BCL2L13|ENSG00000099968|Transcript|ENST00000399777|nonsense_mediated_decay||2/2|ENST00000399777.1:c.*99-7236A>G|||||||rs2535677|1||1|cds_start_NF|SNV|HGNC|17164|||||ENSP00000382677|||UPI0001F77C70||Ensembl|A|A||||||||0.859|0.9092|0.8516|0.9375|0.8121|0.7638||||||||||||0.9375|EAS||||||||||||,G|intron_variant|MODIFIER|BCL2L13|ENSG00000099968|Transcript|ENST00000418951|protein_coding||4/4|ENST00000418951.2:c.*170-7236A>G|||||||rs2535677|1||1||SNV|HGNC|17164|||||ENSP00000410019||Q8IZP5|UPI00000740D0||Ensembl|A|A||||||||0.859|0.9092|0.8516|0.9375|0.8121|0.7638||||||||||||0.9375|EAS||||||||||||,G|intron_variant&non_coding_transcript_variant|MODIFIER|BCL2L13|ENSG00000099968|Transcript|ENST00000485631|processed_transcript||1/1|ENST00000485631.1:n.117-7236A>G|||||||rs2535677|1||1||SNV|HGNC|17164||||||||||Ensembl|A|A||||||||0.859|0.9092|0.8516|0.9375|0.8121|0.7638||||||||||||0.9375|EAS||||||||||||,G|intron_variant&NMD_transcript_variant|MODIFIER|BCL2L13|ENSG00000099968|Transcript|ENST00000498133|nonsense_mediated_decay||5/5|ENST00000498133.1:c.*207-7236A>G|||||||rs2535677|1||1||SNV|HGNC|17164|||||ENSP00000436321||F2Z2C3|UPI000155D5B6||Ensembl|A|A||||||||0.859|0.9092|0.8516|0.9375|0.8121|0.7638||||||||||||0.9375|EAS||||||||||||,G|intron_variant|MODIFIER|BCL2L13|ENSG00000099968|Transcript|ENST00000538149|protein_coding||3/3|ENST00000538149.1:c.229-7236A>G|||||||rs2535677|1||1||SNV|HGNC|17164|||||ENSP00000441344||B7Z238|UPI0001914B19||Ensembl|A|A||||||||0.859|0.9092|0.8516|0.9375|0.8121|0.7638||||||||||||0.9375|EAS||||||||||||,G|intron_variant|MODIFIER|BCL2L13|ENSG00000099968|Transcript|ENST00000543133|protein_coding||5/5|ENST00000543133.1:c.115-7236A>G|||||||rs2535677|1||1||SNV|HGNC|17164||||CCDS59448.1|ENSP00000437667|Q9BXK5||UPI00001A3E35||Ensembl|A|A||||||||0.859|0.9092|0.8516|0.9375|0.8121|0.7638||||||||||||0.9375|EAS||||||||||||,G|intron_variant|MODIFIER|BCL2L13|23786|Transcript|NM_001270726.1|protein_coding||5/5|NM_001270726.1:c.673-7236A>G|||||||rs2535677|1||1||SNV|EntrezGene|17164|||||NP_001257655.1|||||RefSeq|A|A||||||||0.859|0.9092|0.8516|0.9375|0.8121|0.7638||||||||||||0.9375|EAS||||||||||||,G|intron_variant|MODIFIER|BCL2L13|23786|Transcript|NM_001270727.1|protein_coding||4/4|NM_001270727.1:c.529-7236A>G|||||||rs2535677|1||1||SNV|EntrezGene|17164|||||NP_001257656.1|||||RefSeq|A|A||||||||0.859|0.9092|0.8516|0.9375|0.8121|0.7638||||||||||||0.9375|EAS||||||||||||,G|intron_variant|MODIFIER|BCL2L13|23786|Transcript|NM_001270728.1|protein_coding||3/3|NM_001270728.1:c.266-7236A>G|||||||rs2535677|1||1||SNV|EntrezGene|17164|||||NP_001257657.1|||||RefSeq|A|A||||||||0.859|0.9092|0.8516|0.9375|0.8121|0.7638||||||||||||0.9375|EAS||||||||||||,G|intron_variant|MODIFIER|BCL2L13|23786|Transcript|NM_001270729.1|protein_coding||5/5|NM_001270729.1:c.115-7236A>G|||||||rs2535677|1||1||SNV|EntrezGene|17164|||||NP_001257658.1|||||RefSeq|A|A||||||||0.859|0.9092|0.8516|0.9375|0.8121|0.7638||||||||||||0.9375|EAS||||||||||||,G|intron_variant|MODIFIER|BCL2L13|23786|Transcript|NM_001270730.1|protein_coding||4/4|NM_001270730.1:c.115-7236A>G|||||||rs2535677|1||1||SNV|EntrezGene|17164|||||NP_001257659.1|||||RefSeq|A|A||||||||0.859|0.9092|0.8516|0.9375|0.8121|0.7638||||||||||||0.9375|EAS||||||||||||,G|intron_variant|MODIFIER|BCL2L13|23786|Transcript|NM_001270731.1|protein_coding||5/5|NM_001270731.1:c.115-7236A>G|||||||rs2535677|1||1||SNV|EntrezGene|17164|||||NP_001257660.1|||||RefSeq|A|A||||||||0.859|0.9092|0.8516|0.9375|0.8121|0.7638||||||||||||0.9375|EAS||||||||||||,G|intron_variant|MODIFIER|BCL2L13|23786|Transcript|NM_001270732.1|protein_coding||4/4|NM_001270732.1:c.374-7236A>G|||||||rs2535677|1||1||SNV|EntrezGene|17164|||||NP_001257661.1|||||RefSeq|A|A||||||||0.859|0.9092|0.8516|0.9375|0.8121|0.7638||||||||||||0.9375|EAS||||||||||||,G|intron_variant|MODIFIER|BCL2L13|23786|Transcript|NM_001270733.1|protein_coding||1/1|NM_001270733.1:c.-240-7236A>G|||||||rs2535677|1||1||SNV|EntrezGene|17164|||||NP_001257662.1|||||RefSeq|A|A||||||||0.859|0.9092|0.8516|0.9375|0.8121|0.7638||||||||||||0.9375|EAS||||||||||||,G|intron_variant|MODIFIER|BCL2L13|23786|Transcript|NM_001270734.1|protein_coding||4/4|NM_001270734.1:c.387-7236A>G|||||||rs2535677|1||1||SNV|EntrezGene|17164|||||NP_001257663.1|||||RefSeq|A|A||||||||0.859|0.9092|0.8516|0.9375|0.8121|0.7638||||||||||||0.9375|EAS||||||||||||,G|intron_variant|MODIFIER|BCL2L13|23786|Transcript|NM_001270735.1|protein_coding||3/3|NM_001270735.1:c.230-7236A>G|||||||rs2535677|1||1||SNV|EntrezGene|17164|||||NP_001257664.1|||||RefSeq|A|A||||||||0.859|0.9092|0.8516|0.9375|0.8121|0.7638||||||||||||0.9375|EAS||||||||||||,G|intron_variant|MODIFIER|BCL2L13|23786|Transcript|NM_015367.3|protein_coding||6/6|NM_015367.3:c.601-7236A>G|||||||rs2535677|1||1||SNV|EntrezGene|17164|||||NP_056182.2|||||RefSeq|A|A||||||||0.859|0.9092|0.8516|0.9375|0.8121|0.7638||||||||||||0.9375|EAS||||||||||||,G|intron_variant&non_coding_transcript_variant|MODIFIER|BCL2L13|23786|Transcript|NR_073068.1|misc_RNA||4/4|NR_073068.1:n.552-7236A>G|||||||rs2535677|1||1||SNV|EntrezGene|17164||||||||||RefSeq|A|A||||||||0.859|0.9092|0.8516|0.9375|0.8121|0.7638||||||||||||0.9375|EAS||||||||||||,G|intron_variant&non_coding_transcript_variant|MODIFIER|BCL2L13|23786|Transcript|NR_073069.1|misc_RNA||4/4|NR_073069.1:n.535-7236A>G|||||||rs2535677|1||1||SNV|EntrezGene|17164||||||||||RefSeq|A|A||||||||0.859|0.9092|0.8516|0.9375|0.8121|0.7638||||||||||||0.9375|EAS||||||||||||,G|intron_variant|MODIFIER|BCL2L13|23786|Transcript|XM_005261231.1|protein_coding||6/6|XM_005261231.1:c.673-7236A>G|||||||rs2535677|1||1||SNV|EntrezGene|17164|YES||||XP_005261288.1|||||RefSeq|A|A||||||||0.859|0.9092|0.8516|0.9375|0.8121|0.7638||||||||||||0.9375|EAS||||||||||||,G|intron_variant|MODIFIER|BCL2L13|23786|Transcript|XM_005261233.1|protein_coding||5/5|XM_005261233.1:c.374-7236A>G|||||||rs2535677|1||1||SNV|EntrezGene|17164|||||XP_005261290.1|||||RefSeq|A|A||||||||0.859|0.9092|0.8516|0.9375|0.8121|0.7638||||||||||||0.9375|EAS|||||||||||| +22 18225318 22:31882 C T 149858 PASS AC=513;AF=0.855;AN=600;BaseQRankSum=1.66;ClippingRankSum=-0.321;DP=6030;FS=0;GQ_MEAN=86.35;GQ_STDDEV=63.53;HW=0;InbreedingCoeff=-0.0357;MLEAC=515;MLEAF=0.858;MQ=60;MQ0=0;MQRankSum=-0.181;NCC=0;POSITIVE_TRAIN_SITE;QD=26.1;ReadPosRankSum=0.144;SOR=0.713;VQSLOD=3.16;culprit=FS;CSQ=T|intron_variant|MODIFIER|BID|ENSG00000015475|Transcript|ENST00000317361|protein_coding||3/5|ENST00000317361.7:c.361+1251G>A|||||||rs181399|1||-1||SNV|HGNC|1050|YES|||CCDS13747.1|ENSP00000318822|P55957|B2ZP79&B1PL87&A8ASI8|UPI00001D69F1||Ensembl|C|C|||||||||0.8094|0.8256|0.9365|0.8022|0.7822||||||||||||0.9365|EAS||||||||||||,T|intron_variant|MODIFIER|BID|ENSG00000015475|Transcript|ENST00000342111|protein_coding||3/6|ENST00000342111.5:c.223+1251G>A|||||||rs181399|1||-1||SNV|HGNC|1050|||||ENSP00000344594|P55957||UPI00001B5F92||Ensembl|C|C|||||||||0.8094|0.8256|0.9365|0.8022|0.7822||||||||||||0.9365|EAS||||||||||||,T|intron_variant|MODIFIER|BID|ENSG00000015475|Transcript|ENST00000399765|protein_coding||1/3|ENST00000399765.1:c.-65-3064G>A|||||||rs181399|1||-1||SNV|HGNC|1050||||CCDS13749.1|ENSP00000382667|P55957|B2ZP79|UPI00001D69F2||Ensembl|C|C|||||||||0.8094|0.8256|0.9365|0.8022|0.7822||||||||||||0.9365|EAS||||||||||||,T|intron_variant|MODIFIER|BID|ENSG00000015475|Transcript|ENST00000399767|protein_coding||2/4|ENST00000399767.1:c.-66+1251G>A|||||||rs181399|1||-1||SNV|HGNC|1050||||CCDS13749.1|ENSP00000382669|P55957|B2ZP79|UPI00001D69F2||Ensembl|C|C|||||||||0.8094|0.8256|0.9365|0.8022|0.7822||||||||||||0.9365|EAS||||||||||||,T|intron_variant|MODIFIER|BID|ENSG00000015475|Transcript|ENST00000399774|protein_coding||3/5|ENST00000399774.3:c.223+1251G>A|||||||rs181399|1||-1||SNV|HGNC|1050||||CCDS13748.1|ENSP00000382674|P55957|B2ZP79&B1PL87&A8ASI8|UPI0000001637||Ensembl|C|C|||||||||0.8094|0.8256|0.9365|0.8022|0.7822||||||||||||0.9365|EAS||||||||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|BID|ENSG00000015475|Transcript|ENST00000473439|processed_transcript||2/3|ENST00000473439.1:n.326+1251G>A|||||||rs181399|1||-1||SNV|HGNC|1050||||||||||Ensembl|C|C|||||||||0.8094|0.8256|0.9365|0.8022|0.7822||||||||||||0.9365|EAS||||||||||||,T|upstream_gene_variant|MODIFIER|BID|ENSG00000015475|Transcript|ENST00000494097|retained_intron||||||||||rs181399|1|1358|-1||SNV|HGNC|1050||||||||||Ensembl|C|C|||||||||0.8094|0.8256|0.9365|0.8022|0.7822||||||||||||0.9365|EAS||||||||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|BID|ENSG00000015475|Transcript|ENST00000550946|retained_intron||3/5|ENST00000550946.1:n.313+1251G>A|||||||rs181399|1||-1||SNV|HGNC|1050||||||||||Ensembl|C|C|||||||||0.8094|0.8256|0.9365|0.8022|0.7822||||||||||||0.9365|EAS||||||||||||,T|intron_variant|MODIFIER|BID|ENSG00000015475|Transcript|ENST00000551952|protein_coding||3/5|ENST00000551952.1:c.223+1251G>A|||||||rs181399|1||-1||SNV|HGNC|1050||||CCDS13748.1|ENSP00000449236|P55957|B2ZP79&B1PL87&A8ASI8|UPI0000001637||Ensembl|C|C|||||||||0.8094|0.8256|0.9365|0.8022|0.7822||||||||||||0.9365|EAS||||||||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|BID|ENSG00000015475|Transcript|ENST00000552886|processed_transcript||2/2|ENST00000552886.1:n.289+1251G>A|||||||rs181399|1||-1||SNV|HGNC|1050||||||||||Ensembl|C|C|||||||||0.8094|0.8256|0.9365|0.8022|0.7822||||||||||||0.9365|EAS||||||||||||,T|intron_variant|MODIFIER|BID|637|Transcript|NM_001196.3|protein_coding||3/5|NM_001196.3:c.223+1251G>A|||||||rs181399|1||-1||SNV|EntrezGene|1050|||||NP_001187.1|||||RefSeq|C|C|OK||||||||0.8094|0.8256|0.9365|0.8022|0.7822||||||||||||0.9365|EAS||||||||||||,T|intron_variant|MODIFIER|BID|637|Transcript|NM_001244567.1|protein_coding||3/5|NM_001244567.1:c.223+1251G>A|||||||rs181399|1||-1||SNV|EntrezGene|1050|||||NP_001231496.1|||||RefSeq|C|C|OK||||||||0.8094|0.8256|0.9365|0.8022|0.7822||||||||||||0.9365|EAS||||||||||||,T|intron_variant|MODIFIER|BID|637|Transcript|NM_001244569.1|protein_coding||2/4|NM_001244569.1:c.-65-3064G>A|||||||rs181399|1||-1||SNV|EntrezGene|1050|||||NP_001231498.1|||||RefSeq|C|C|OK||||||||0.8094|0.8256|0.9365|0.8022|0.7822||||||||||||0.9365|EAS||||||||||||,T|intron_variant|MODIFIER|BID|637|Transcript|NM_001244570.1|protein_coding||1/3|NM_001244570.1:c.-65-3064G>A|||||||rs181399|1||-1||SNV|EntrezGene|1050|||||NP_001231499.1|||||RefSeq|C|C|OK||||||||0.8094|0.8256|0.9365|0.8022|0.7822||||||||||||0.9365|EAS||||||||||||,T|intron_variant|MODIFIER|BID|637|Transcript|NM_001244572.1|protein_coding||1/3|NM_001244572.1:c.-65-3064G>A|||||||rs181399|1||-1||SNV|EntrezGene|1050|||||NP_001231501.1|||||RefSeq|C|C|OK||||||||0.8094|0.8256|0.9365|0.8022|0.7822||||||||||||0.9365|EAS||||||||||||,T|intron_variant|MODIFIER|BID|637|Transcript|NM_197966.2|protein_coding||3/5|NM_197966.2:c.361+1251G>A|||||||rs181399|1||-1||SNV|EntrezGene|1050|YES||||NP_932070.1|||||RefSeq|C|C|OK||||||||0.8094|0.8256|0.9365|0.8022|0.7822||||||||||||0.9365|EAS||||||||||||,T|intron_variant|MODIFIER|BID|637|Transcript|NM_197967.2|protein_coding||2/4|NM_197967.2:c.-66+1251G>A|||||||rs181399|1||-1||SNV|EntrezGene|1050|||||NP_932071.1|||||RefSeq|C|C|OK||||||||0.8094|0.8256|0.9365|0.8022|0.7822||||||||||||0.9365|EAS||||||||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|BID|637|Transcript|XR_244338.1|misc_RNA||3/6|XR_244338.1:n.390+1251G>A|||||||rs181399|1||-1||SNV|EntrezGene|1050||||||||||RefSeq|C|C|||||||||0.8094|0.8256|0.9365|0.8022|0.7822||||||||||||0.9365|EAS||||||||||||,T|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000301067|CTCF_binding_site||||||||||rs181399|1||||SNV|||||||||||||||||||||||0.8094|0.8256|0.9365|0.8022|0.7822||||||||||||0.9365|EAS||||||||||||,T|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00523333330|||||||||||rs181399|1||1||SNV|||||||||||||||||||||||0.8094|0.8256|0.9365|0.8022|0.7822||||||||||||0.9365|EAS|||||ENSM00523333330|14|N|-0.025||||,T|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00523966268|||||||||||rs181399|1||1||SNV|||||||||||||||||||||||0.8094|0.8256|0.9365|0.8022|0.7822||||||||||||0.9365|EAS|||||ENSM00523966268|4|N|-0.005||||,T|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00525592001|||||||||||rs181399|1||1||SNV|||||||||||||||||||||||0.8094|0.8256|0.9365|0.8022|0.7822||||||||||||0.9365|EAS|||||ENSM00525592001|1|N|-0.027|||| +22 18229774 22:31915 T C 221760 PASS AC=517;AF=0.862;AN=600;BaseQRankSum=-1.026;ClippingRankSum=0.254;DP=9401;FS=0;GQ_MEAN=141.85;GQ_STDDEV=102.66;HW=0.2;InbreedingCoeff=-0.0207;MLEAC=517;MLEAF=0.862;MQ=60;MQ0=0;MQRankSum=-0.021;NCC=0;POSITIVE_TRAIN_SITE;QD=24.32;ReadPosRankSum=0.19;SOR=0.695;VQSLOD=7.22;culprit=FS;CSQ=C|intron_variant|MODIFIER|BID|ENSG00000015475|Transcript|ENST00000317361|protein_coding||2/5|ENST00000317361.7:c.151-2995A>G|||||||rs181402|1||-1||SNV|HGNC|1050|YES|||CCDS13747.1|ENSP00000318822|P55957|B2ZP79&B1PL87&A8ASI8|UPI00001D69F1||Ensembl|T|T||||||||0.8552|0.9009|0.83|0.9385|0.8012|0.7812||||||||||||0.9385|EAS||||||||||||,C|intron_variant|MODIFIER|BID|ENSG00000015475|Transcript|ENST00000342111|protein_coding||2/6|ENST00000342111.5:c.13-2995A>G|||||||rs181402|1||-1||SNV|HGNC|1050|||||ENSP00000344594|P55957||UPI00001B5F92||Ensembl|T|T||||||||0.8552|0.9009|0.83|0.9385|0.8012|0.7812||||||||||||0.9385|EAS||||||||||||,C|intron_variant|MODIFIER|BID|ENSG00000015475|Transcript|ENST00000399765|protein_coding||1/3|ENST00000399765.1:c.-65-7520A>G|||||||rs181402|1||-1||SNV|HGNC|1050||||CCDS13749.1|ENSP00000382667|P55957|B2ZP79|UPI00001D69F2||Ensembl|T|T||||||||0.8552|0.9009|0.83|0.9385|0.8012|0.7812||||||||||||0.9385|EAS||||||||||||,C|intron_variant|MODIFIER|BID|ENSG00000015475|Transcript|ENST00000399767|protein_coding||1/4|ENST00000399767.1:c.-276-2995A>G|||||||rs181402|1||-1||SNV|HGNC|1050||||CCDS13749.1|ENSP00000382669|P55957|B2ZP79|UPI00001D69F2||Ensembl|T|T||||||||0.8552|0.9009|0.83|0.9385|0.8012|0.7812||||||||||||0.9385|EAS||||||||||||,C|intron_variant|MODIFIER|BID|ENSG00000015475|Transcript|ENST00000399774|protein_coding||2/5|ENST00000399774.3:c.13-2995A>G|||||||rs181402|1||-1||SNV|HGNC|1050||||CCDS13748.1|ENSP00000382674|P55957|B2ZP79&B1PL87&A8ASI8|UPI0000001637||Ensembl|T|T||||||||0.8552|0.9009|0.83|0.9385|0.8012|0.7812||||||||||||0.9385|EAS||||||||||||,C|intron_variant&non_coding_transcript_variant|MODIFIER|BID|ENSG00000015475|Transcript|ENST00000473439|processed_transcript||1/3|ENST00000473439.1:n.116-2995A>G|||||||rs181402|1||-1||SNV|HGNC|1050||||||||||Ensembl|T|T||||||||0.8552|0.9009|0.83|0.9385|0.8012|0.7812||||||||||||0.9385|EAS||||||||||||,C|intron_variant&non_coding_transcript_variant|MODIFIER|BID|ENSG00000015475|Transcript|ENST00000550946|retained_intron||2/5|ENST00000550946.1:n.103-2995A>G|||||||rs181402|1||-1||SNV|HGNC|1050||||||||||Ensembl|T|T||||||||0.8552|0.9009|0.83|0.9385|0.8012|0.7812||||||||||||0.9385|EAS||||||||||||,C|intron_variant|MODIFIER|BID|ENSG00000015475|Transcript|ENST00000551952|protein_coding||2/5|ENST00000551952.1:c.13-2995A>G|||||||rs181402|1||-1||SNV|HGNC|1050||||CCDS13748.1|ENSP00000449236|P55957|B2ZP79&B1PL87&A8ASI8|UPI0000001637||Ensembl|T|T||||||||0.8552|0.9009|0.83|0.9385|0.8012|0.7812||||||||||||0.9385|EAS||||||||||||,C|intron_variant&non_coding_transcript_variant|MODIFIER|BID|ENSG00000015475|Transcript|ENST00000552886|processed_transcript||1/2|ENST00000552886.1:n.79-2995A>G|||||||rs181402|1||-1||SNV|HGNC|1050||||||||||Ensembl|T|T||||||||0.8552|0.9009|0.83|0.9385|0.8012|0.7812||||||||||||0.9385|EAS||||||||||||,C|intron_variant|MODIFIER|BID|637|Transcript|NM_001196.3|protein_coding||2/5|NM_001196.3:c.13-2995A>G|||||||rs181402|1||-1||SNV|EntrezGene|1050|||||NP_001187.1|||||RefSeq|T|T|OK|||||||0.8552|0.9009|0.83|0.9385|0.8012|0.7812||||||||||||0.9385|EAS||||||||||||,C|intron_variant|MODIFIER|BID|637|Transcript|NM_001244567.1|protein_coding||2/5|NM_001244567.1:c.13-2995A>G|||||||rs181402|1||-1||SNV|EntrezGene|1050|||||NP_001231496.1|||||RefSeq|T|T|OK|||||||0.8552|0.9009|0.83|0.9385|0.8012|0.7812||||||||||||0.9385|EAS||||||||||||,C|intron_variant|MODIFIER|BID|637|Transcript|NM_001244569.1|protein_coding||2/4|NM_001244569.1:c.-66+3097A>G|||||||rs181402|1||-1||SNV|EntrezGene|1050|||||NP_001231498.1|||||RefSeq|T|T|OK|||||||0.8552|0.9009|0.83|0.9385|0.8012|0.7812||||||||||||0.9385|EAS||||||||||||,C|intron_variant|MODIFIER|BID|637|Transcript|NM_001244570.1|protein_coding||1/3|NM_001244570.1:c.-65-7520A>G|||||||rs181402|1||-1||SNV|EntrezGene|1050|||||NP_001231499.1|||||RefSeq|T|T|OK|||||||0.8552|0.9009|0.83|0.9385|0.8012|0.7812||||||||||||0.9385|EAS||||||||||||,C|intron_variant|MODIFIER|BID|637|Transcript|NM_001244572.1|protein_coding||1/3|NM_001244572.1:c.-65-7520A>G|||||||rs181402|1||-1||SNV|EntrezGene|1050|||||NP_001231501.1|||||RefSeq|T|T|OK|||||||0.8552|0.9009|0.83|0.9385|0.8012|0.7812||||||||||||0.9385|EAS||||||||||||,C|intron_variant|MODIFIER|BID|637|Transcript|NM_197966.2|protein_coding||2/5|NM_197966.2:c.151-2995A>G|||||||rs181402|1||-1||SNV|EntrezGene|1050|YES||||NP_932070.1|||||RefSeq|T|T|OK|||||||0.8552|0.9009|0.83|0.9385|0.8012|0.7812||||||||||||0.9385|EAS||||||||||||,C|intron_variant|MODIFIER|BID|637|Transcript|NM_197967.2|protein_coding||1/4|NM_197967.2:c.-276-2995A>G|||||||rs181402|1||-1||SNV|EntrezGene|1050|||||NP_932071.1|||||RefSeq|T|T|OK|||||||0.8552|0.9009|0.83|0.9385|0.8012|0.7812||||||||||||0.9385|EAS||||||||||||,C|intron_variant&non_coding_transcript_variant|MODIFIER|BID|637|Transcript|XR_244338.1|misc_RNA||2/6|XR_244338.1:n.180-2995A>G|||||||rs181402|1||-1||SNV|EntrezGene|1050||||||||||RefSeq|T|T||||||||0.8552|0.9009|0.83|0.9385|0.8012|0.7812||||||||||||0.9385|EAS|||||||||||| diff --git a/scripts/importer/tests/data/dataset1_1_coverage.txt b/scripts/importer/tests/data/dataset1_1_coverage.txt new file mode 100644 index 000000000..01547951f --- /dev/null +++ b/scripts/importer/tests/data/dataset1_1_coverage.txt @@ -0,0 +1,26 @@ +#chrom pos mean median 1 5 10 15 20 25 30 50 100 +22 46515890 37.84 37 1.00 1.00 1.00 1.00 0.99 0.96 0.86 0.08 0.00 +22 46515900 38.02 37 1.00 1.00 1.00 1.00 0.99 0.97 0.85 0.08 0.00 +22 46515910 37.97 38 1.00 1.00 1.00 1.00 0.99 0.96 0.85 0.09 0.00 +22 46515920 38.27 38 1.00 1.00 1.00 1.00 0.99 0.96 0.87 0.08 0.00 +22 46515930 38.40 38 1.00 1.00 1.00 1.00 0.99 0.96 0.86 0.10 0.00 +22 46515940 38.53 38 1.00 1.00 1.00 1.00 1.00 0.95 0.87 0.10 0.00 +22 46515950 38.05 38 1.00 1.00 1.00 1.00 0.99 0.94 0.87 0.11 0.00 +22 46515960 37.99 37 1.00 1.00 1.00 1.00 1.00 0.95 0.85 0.12 0.00 +22 46515970 37.90 37 1.00 1.00 1.00 1.00 0.99 0.96 0.86 0.11 0.00 +22 46515980 37.49 37 1.00 1.00 1.00 1.00 0.99 0.93 0.85 0.09 0.00 +22 46515990 37.91 37 1.00 1.00 1.00 1.00 0.99 0.95 0.83 0.10 0.00 +22 46516000 37.63 37 1.00 1.00 1.00 1.00 0.99 0.95 0.82 0.10 0.00 +22 46516010 37.70 37 1.00 1.00 1.00 1.00 0.99 0.95 0.83 0.09 0.00 +22 46516020 37.63 37 1.00 1.00 1.00 1.00 0.99 0.95 0.84 0.09 0.00 +22 46516030 37.88 37 1.00 1.00 1.00 1.00 0.99 0.96 0.86 0.08 0.00 +22 46516040 37.06 36 1.00 1.00 1.00 1.00 0.99 0.94 0.83 0.07 0.00 +22 46516050 36.34 36 1.00 1.00 1.00 1.00 0.99 0.93 0.80 0.06 0.00 +22 46516060 36.28 36 1.00 1.00 1.00 1.00 0.99 0.93 0.80 0.06 0.00 +22 46516070 35.86 35 1.00 1.00 1.00 1.00 0.99 0.94 0.78 0.06 0.00 +22 46516080 35.38 35 1.00 1.00 1.00 1.00 0.99 0.94 0.78 0.06 0.00 +22 46516090 35.19 34 1.00 1.00 1.00 1.00 0.99 0.93 0.76 0.06 0.00 +22 46516100 34.88 34 1.00 1.00 1.00 1.00 1.00 0.92 0.75 0.04 0.00 +22 46516110 35.14 35 1.00 1.00 1.00 1.00 0.99 0.92 0.78 0.05 0.00 +22 46516120 35.20 34 1.00 1.00 1.00 1.00 1.00 0.94 0.79 0.05 0.00 +22 46516130 35.28 35 1.00 1.00 1.00 1.00 0.99 0.93 0.76 0.05 0.00 diff --git a/scripts/importer/tests/data/dataset1_2.vcf b/scripts/importer/tests/data/dataset1_2.vcf new file mode 100644 index 000000000..e573e4b81 --- /dev/null +++ b/scripts/importer/tests/data/dataset1_2.vcf @@ -0,0 +1,160 @@ +##ALT= +#CHROM POS ID REF ALT QUAL FILTER INFO +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##fileformat=VCFv4.2 +##FILTER= +##FILTER= +##FILTER= +##FILTER= +##FILTER= +##FILTER= +##FILTER= +##FILTER= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##GVCFBlock=minGQ=0(inclusive),maxGQ=1(exclusive) +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##LoF_filter=Reason for LoF not being HC +##LoF_flags=Possible warning flags for LoF +##LoF_info=Info used for LoF annotation +##LoF=Loss-of-function annotation (HC = High Confidence; LC = Low Confidence) +##reference=file:///sw/data/uppnex/reference/biodata/GATK/ftp.broadinstitute.org/bundle/2.8/b37/human_g1k_v37.fasta +##VEP=v84 db=. polyphen=2.2.2 genebuild=2011-04 dbSNP=144 gencode=GENCODE 19 regbuild=13 HGMD-PUBLIC=20152 sift=sift5.2.2 assembly=GRCh37.p13 COSMIC=71 ClinVar=201507 ESP=20141103 +22 16263767 rs2716251 G A 568432 VQSRTrancheSNP99.90to100.00 AC=1377;AF=0.689;AN=2000;BaseQRankSum=-0.027;ClippingRankSum=-0.044;DB;DP=36470;ExcessHet=2.14748e+09;FS=83.243;MLEAC=1380;MLEAF=0.69;MQ=37.4;MQ0=0;MQRankSum=-4.06;QD=15.79;ReadPosRankSum=0.17;SOR=3.693;VQSLOD=-41.68;culprit=FS;AC_Het=605;AC_Hom=772;AC_Hemi=0;AN_Adj=2000;AN_KGA=2000;AC_Adj=1377;AC_KGA=1377;Hom_KGA=772;Het_KGA=605;Hemi_KGA=0;CSQ=A|intron_variant|MODIFIER|POTEH|ENSG00000198062|Transcript|ENST00000343518|protein_coding||9/10|ENST00000343518.6:c.1520+3162C>T|||||||rs2154837|1||-1||SNV|HGNC|133|YES|||CCDS46658.1|ENSP00000340610|POTEH_HUMAN||UPI0000E5A425||||||||||||||||||||||||||||||||||,A|intron_variant&NMD_transcript_variant|MODIFIER|POTEH|ENSG00000198062|Transcript|ENST00000452800|nonsense_mediated_decay||10/11|ENST00000452800.1:c.*696+3162C>T|||||||rs2154837|1||-1|cds_start_NF|SNV|HGNC|133|||||ENSP00000442107||H0YG78_HUMAN|UPI000204A808|||||||||||||||||||||||||||||||||| +22 16283300 rs200045958 G A 512760 VQSRTrancheSNP99.90to100.00 AC=1347;AF=0.678;AN=1986;BaseQRankSum=1.45;ClippingRankSum=0.062;DB;DP=31551;ExcessHet=2.14748e+09;FS=0;InbreedingCoeff=-0.3905;MLEAC=1349;MLEAF=0.679;MQ=26.1;MQ0=0;MQRankSum=-0.491;QD=16.48;ReadPosRankSum=0.668;SOR=0.706;VQSLOD=-49.54;culprit=MQ;AC_Het=601;AC_Hom=746;AC_Hemi=0;AN_Adj=1986;AN_KGA=1986;AC_Adj=1347;AC_KGA=1347;Hom_KGA=746;Het_KGA=601;Hemi_KGA=0;CSQ=A|downstream_gene_variant|MODIFIER|POTEH-AS1|ENSG00000236666|Transcript|ENST00000422014|antisense||||||||||rs200045958&rs8138383|1|4698|1||SNV|HGNC|40058|YES|||||||||||||G:0.3051|A:0.5862&A:0.5862|A:0.7118&A:0.7118|A:0.7827&A:0.7827|A:0.6849&A:0.6849|A:0.7495&A:0.7495|||||||||||||||||||||||,A|intron_variant|MODIFIER|POTEH|ENSG00000198062|Transcript|ENST00000343518|protein_coding||1/10|ENST00000343518.6:c.633-708C>T|||||||rs200045958&rs8138383|1||-1||SNV|HGNC|133|YES|||CCDS46658.1|ENSP00000340610|POTEH_HUMAN||UPI0000E5A425||||||G:0.3051|A:0.5862&A:0.5862|A:0.7118&A:0.7118|A:0.7827&A:0.7827|A:0.6849&A:0.6849|A:0.7495&A:0.7495|||||||||||||||||||||||,A|intron_variant&NMD_transcript_variant|MODIFIER|POTEH|ENSG00000198062|Transcript|ENST00000452800|nonsense_mediated_decay||1/11|ENST00000452800.1:c.465-708C>T|||||||rs200045958&rs8138383|1||-1|cds_start_NF|SNV|HGNC|133|||||ENSP00000442107||H0YG78_HUMAN|UPI000204A808||||||G:0.3051|A:0.5862&A:0.5862|A:0.7118&A:0.7118|A:0.7827&A:0.7827|A:0.6849&A:0.6849|A:0.7495&A:0.7495||||||||||||||||||||||| +22 16285350 rs116260054 G C 174358 VQSRTrancheSNP99.90to100.00 AC=976;AF=0.587;AN=1662;BaseQRankSum=1.63;ClippingRankSum=-0.045;DB;DP=16983;ExcessHet=0.1397;FS=180.887;MLEAC=975;MLEAF=0.587;MQ=40.44;MQ0=0;MQRankSum=-2.69;QD=12.92;ReadPosRankSum=0.58;SOR=9.706;VQSLOD=-23780;culprit=FS;AC_Het=364;AC_Hom=612;AC_Hemi=0;AN_Adj=1662;AN_KGA=1662;AC_Adj=976;AC_KGA=976;Hom_KGA=612;Het_KGA=364;Hemi_KGA=0;CSQ=C|intron_variant|MODIFIER|POTEH|ENSG00000198062|Transcript|ENST00000343518|protein_coding||1/10|ENST00000343518.6:c.632+1904C>G|||||||rs116260054|1||-1||SNV|HGNC|133|YES|||CCDS46658.1|ENSP00000340610|POTEH_HUMAN||UPI0000E5A425||||||C:0.2977|C:0.4697|C:0.2133|C:0.1855|C:0.2266|C:0.3139|||||||||||||||||||||||,C|intron_variant&NMD_transcript_variant|MODIFIER|POTEH|ENSG00000198062|Transcript|ENST00000452800|nonsense_mediated_decay||1/11|ENST00000452800.1:c.464+1904C>G|||||||rs116260054|1||-1|cds_start_NF|SNV|HGNC|133|||||ENSP00000442107||H0YG78_HUMAN|UPI000204A808||||||C:0.2977|C:0.4697|C:0.2133|C:0.1855|C:0.2266|C:0.3139||||||||||||||||||||||| +22 16286239 rs201077540 A G 391206 VQSRTrancheSNP99.90to100.00 AC=975;AF=0.488;AN=1998;BaseQRankSum=-0.39;ClippingRankSum=-0.12;DB;DP=43446;ExcessHet=2.14748e+09;FS=19.445;InbreedingCoeff=-0.368;MLEAC=988;MLEAF=0.494;MQ=36.03;MQ0=0;MQRankSum=-1.85;QD=11.26;ReadPosRankSum=0.196;SOR=1.746;VQSLOD=-26.92;culprit=MQ;AC_Het=671;AC_Hom=304;AC_Hemi=0;AN_Adj=1998;AN_KGA=1998;AC_Adj=975;AC_KGA=975;Hom_KGA=304;Het_KGA=671;Hemi_KGA=0;CSQ=G|intron_variant|MODIFIER|POTEH|ENSG00000198062|Transcript|ENST00000343518|protein_coding||1/10|ENST00000343518.6:c.632+1015T>C|||||||rs62224837|1||-1||SNV|HGNC|133|YES|||CCDS46658.1|ENSP00000340610|POTEH_HUMAN||UPI0000E5A425||||||||||||||||||||||||||||||||||,G|intron_variant&NMD_transcript_variant|MODIFIER|POTEH|ENSG00000198062|Transcript|ENST00000452800|nonsense_mediated_decay||1/11|ENST00000452800.1:c.464+1015T>C|||||||rs62224837|1||-1|cds_start_NF|SNV|HGNC|133|||||ENSP00000442107||H0YG78_HUMAN|UPI000204A808|||||||||||||||||||||||||||||||||| +22 16288255 rs371907891 T C,TGCCAAGCCAAGCAAAGAAC 605667 VQSRTrancheINDEL99.90to100.00 AC=989,1;AF=0.495,0.0005;AN=2000;BaseQRankSum=-0.618;ClippingRankSum=-0.041;DB;DP=78349;ExcessHet=2.14748e+09;FS=112.401;InbreedingCoeff=-4.4727;MLEAC=990,1;MLEAF=0.495,0.0005;MQ=47.54;MQ0=0;MQRankSum=-4.794;QD=7.93;ReadPosRankSum=0.83;SOR=9.019;VQSLOD=-20.53;culprit=FS;AC_Het=985,1;AC_Hom=4,0;AC_Hemi=0,0;AN_Adj=2000;AN_KGA=2000;AC_Adj=989,1;AC_KGA=989,1;Hom_KGA=4,0;Het_KGA=985,1;Hemi_KGA=0,0;CSQ=C|upstream_gene_variant|MODIFIER|POTEH|ENSG00000198062|Transcript|ENST00000452800|nonsense_mediated_decay||||||||||rs371907891|1|538|-1|cds_start_NF|indel|HGNC|133|||||ENSP00000442107||H0YG78_HUMAN|UPI000204A808||||||||||||||||||||||||||||||||||,TGCCAAGCCAAGCAAAGAAC|upstream_gene_variant|MODIFIER|POTEH|ENSG00000198062|Transcript|ENST00000452800|nonsense_mediated_decay||||||||||rs371907891|2|538|-1|cds_start_NF|indel|HGNC|133|||||ENSP00000442107||H0YG78_HUMAN|UPI000204A808||||||||||||||||||||||||||||||||||,C|upstream_gene_variant|MODIFIER|POTEH|ENSG00000198062|Transcript|ENST00000343518|protein_coding||||||||||rs371907891|1|318|-1||indel|HGNC|133|YES|||CCDS46658.1|ENSP00000340610|POTEH_HUMAN||UPI0000E5A425||||||||||||||||||||||||||||||||||,TGCCAAGCCAAGCAAAGAAC|upstream_gene_variant|MODIFIER|POTEH|ENSG00000198062|Transcript|ENST00000343518|protein_coding||||||||||rs371907891|2|318|-1||indel|HGNC|133|YES|||CCDS46658.1|ENSP00000340610|POTEH_HUMAN||UPI0000E5A425|||||||||||||||||||||||||||||||||| +22 16288538 rs62224840 T C,TGGCGTGCGCGCGC,* 1.44549e+06 PASS AC=1212,584,2;AF=0.614,0.296,0.001013;AN=1974;BaseQRankSum=-0.687;ClippingRankSum=0.208;DB;DP=59434;ExcessHet=39.4521;FS=2.597;MLEAC=1212,584,2;MLEAF=0.614,0.296,0.001013;MQ=55.58;MQ0=0;MQRankSum=-0.484;NEGATIVE_TRAIN_SITE;QD=33.83;ReadPosRankSum=0.883;SOR=0.341;VQSLOD=-1.577;culprit=FS;AC_Het=700,578,2;AC_Hom=512,6,0;AC_Hemi=0,0,0;AN_Adj=1974;AN_KGA=1974;AC_Adj=1212,584,2;AC_KGA=1212,584,2;Hom_KGA=512,6,0;Het_KGA=700,578,2;Hemi_KGA=0,0,0;CSQ=C|upstream_gene_variant|MODIFIER|POTEH|ENSG00000198062|Transcript|ENST00000452800|nonsense_mediated_decay||||||||||rs62224840|1|821|-1|cds_start_NF|sequence_alteration|HGNC|133|||||ENSP00000442107||H0YG78_HUMAN|UPI000204A808||||||||||||||||||||||||||||||||||,TGGCGTGCGCGCGC|upstream_gene_variant|MODIFIER|POTEH|ENSG00000198062|Transcript|ENST00000452800|nonsense_mediated_decay||||||||||rs62224840|2|821|-1|cds_start_NF|sequence_alteration|HGNC|133|||||ENSP00000442107||H0YG78_HUMAN|UPI000204A808||||||||||||||||||||||||||||||||||,C|upstream_gene_variant|MODIFIER|POTEH|ENSG00000198062|Transcript|ENST00000343518|protein_coding||||||||||rs62224840|1|601|-1||sequence_alteration|HGNC|133|YES|||CCDS46658.1|ENSP00000340610|POTEH_HUMAN||UPI0000E5A425||||||||||||||||||||||||||||||||||,TGGCGTGCGCGCGC|upstream_gene_variant|MODIFIER|POTEH|ENSG00000198062|Transcript|ENST00000343518|protein_coding||||||||||rs62224840|2|601|-1||sequence_alteration|HGNC|133|YES|||CCDS46658.1|ENSP00000340610|POTEH_HUMAN||UPI0000E5A425|||||||||||||||||||||||||||||||||| +22 16288742 rs76462367 G C 1.00504e+06 VQSRTrancheSNP99.00to99.90 AC=1334;AF=0.702;AN=1900;BaseQRankSum=-0.389;ClippingRankSum=-0.06;DB;DP=35702;ExcessHet=2.14748e+09;FS=2.885;InbreedingCoeff=-0.287;MLEAC=1359;MLEAF=0.715;MQ=53.32;MQ0=0;MQRankSum=-2.757;NEGATIVE_TRAIN_SITE;QD=30.51;ReadPosRankSum=0.231;SOR=0.944;VQSLOD=-3.356;culprit=MQRankSum;AC_Het=490;AC_Hom=844;AC_Hemi=0;AN_Adj=1900;AN_KGA=1900;AC_Adj=1334;AC_KGA=1334;Hom_KGA=844;Het_KGA=490;Hemi_KGA=0;CSQ=C|upstream_gene_variant|MODIFIER|POTEH|ENSG00000198062|Transcript|ENST00000343518|protein_coding||||||||||rs76462367|1|805|-1||SNV|HGNC|133|YES|||CCDS46658.1|ENSP00000340610|POTEH_HUMAN||UPI0000E5A425||||||G:0.2065|C:0.8964|C:0.7695|C:0.6776|C:0.7803|C:0.8047|||||||||||||||||||||||,C|upstream_gene_variant|MODIFIER|POTEH|ENSG00000198062|Transcript|ENST00000452800|nonsense_mediated_decay||||||||||rs76462367|1|1025|-1|cds_start_NF|SNV|HGNC|133|||||ENSP00000442107||H0YG78_HUMAN|UPI000204A808||||||G:0.2065|C:0.8964|C:0.7695|C:0.6776|C:0.7803|C:0.8047||||||||||||||||||||||| +22 16288776 rs67775324 A G 1.0032e+06 VQSRTrancheSNP99.00to99.90 AC=1320;AF=0.7;AN=1886;BaseQRankSum=-2.381;ClippingRankSum=-0.051;DB;DP=39005;ExcessHet=138.447;FS=1.301;InbreedingCoeff=-0.2566;MLEAC=1351;MLEAF=0.716;MQ=52.63;MQ0=0;MQRankSum=-3.055;NEGATIVE_TRAIN_SITE;QD=28.38;ReadPosRankSum=-0.224;SOR=0.798;VQSLOD=-3.749;culprit=MQRankSum;AC_Het=470;AC_Hom=850;AC_Hemi=0;AN_Adj=1886;AN_KGA=1886;AC_Adj=1320;AC_KGA=1320;Hom_KGA=850;Het_KGA=470;Hemi_KGA=0;CSQ=G|upstream_gene_variant|MODIFIER|POTEH|ENSG00000198062|Transcript|ENST00000452800|nonsense_mediated_decay||||||||||rs67775324|1|1059|-1|cds_start_NF|SNV|HGNC|133|||||ENSP00000442107||H0YG78_HUMAN|UPI000204A808||||||||||||||||||||||||||||||||||,G|upstream_gene_variant|MODIFIER|POTEH|ENSG00000198062|Transcript|ENST00000343518|protein_coding||||||||||rs67775324|1|839|-1||SNV|HGNC|133|YES|||CCDS46658.1|ENSP00000340610|POTEH_HUMAN||UPI0000E5A425|||||||||||||||||||||||||||||||||| +22 16364923 rs5771604 C A 967564 VQSRTrancheSNP99.00to99.90 AC=1057;AF=0.529;AN=2000;BaseQRankSum=0.642;ClippingRankSum=-0.058;DB;DP=50352;ExcessHet=2.14748e+09;FS=8.487;MLEAC=1060;MLEAF=0.53;MQ=53.71;MQ0=0;MQRankSum=-3.951;NEGATIVE_TRAIN_SITE;QD=19.96;ReadPosRankSum=-0.32;SOR=1.241;VQSLOD=-5.859;culprit=MQRankSum;AC_Het=835;AC_Hom=222;AC_Hemi=0;AN_Adj=2000;AN_KGA=2000;AC_Adj=1057;AC_KGA=1057;Hom_KGA=222;Het_KGA=835;Hemi_KGA=0;CSQ=A|downstream_gene_variant|MODIFIER|LA16c-2F2.5|ENSG00000226474|Transcript|ENST00000440999|unprocessed_pseudogene||||||||||rs5771604|1|2362|1||SNV|Clone_based_vega_gene||YES|||||||||||||C:0.4599|A:0.8442|A:0.4582|A:0.3363|A:0.4612|A:0.4785|||||||||||||||||||||||,A|non_coding_transcript_exon_variant&non_coding_transcript_variant|MODIFIER|NEK2P2|ENSG00000231565|Transcript|ENST00000438441|processed_pseudogene|1/1||ENST00000438441.1:n.57C>A||57|||||rs5771604|1||1||SNV|HGNC|37816|YES|||||||||||||C:0.4599|A:0.8442|A:0.4582|A:0.3363|A:0.4612|A:0.4785||||||||||||||||||||||| +22 16365289 rs141818524 G A 344637 VQSRTrancheSNP99.90to100.00 AC=1662;AF=0.833;AN=1996;BaseQRankSum=-0.392;ClippingRankSum=0;DB;DP=17926;ExcessHet=0.0975;FS=22.413;MLEAC=1678;MLEAF=0.841;MQ=32.1;MQ0=0;MQRankSum=-3.254;QD=20.78;ReadPosRankSum=0.504;SOR=1.911;VQSLOD=-32.66;culprit=MQ;AC_Het=256;AC_Hom=1406;AC_Hemi=0;AN_Adj=1996;AN_KGA=1996;AC_Adj=1662;AC_KGA=1662;Hom_KGA=1406;Het_KGA=256;Hemi_KGA=0;CSQ=A|downstream_gene_variant|MODIFIER|LA16c-2F2.5|ENSG00000226474|Transcript|ENST00000440999|unprocessed_pseudogene||||||||||rs1153411|1|2728|1||SNV|Clone_based_vega_gene||YES|||||||||||||G:0.2520|A:0.9191|A:0.6888|A:0.6895|A:0.6899|A:0.6789|||||||||||||||||||||||,A|non_coding_transcript_exon_variant&non_coding_transcript_variant|MODIFIER|NEK2P2|ENSG00000231565|Transcript|ENST00000438441|processed_pseudogene|1/1||ENST00000438441.1:n.423G>A||423|||||rs1153411|1||1||SNV|HGNC|37816|YES|||||||||||||G:0.2520|A:0.9191|A:0.6888|A:0.6895|A:0.6899|A:0.6789||||||||||||||||||||||| +22 16370229 rs371958062 G A 858332 VQSRTrancheSNP99.90to100.00 AC=974;AF=0.487;AN=2000;BaseQRankSum=-0.428;ClippingRankSum=0.059;DB;DP=77999;ExcessHet=2.14748e+09;FS=3.256;MLEAC=978;MLEAF=0.489;MQ=32.13;MQ0=0;MQRankSum=-1.564;QD=11.19;ReadPosRankSum=0.623;SOR=0.973;VQSLOD=-44.14;culprit=MQ;AC_Het=974;AC_Hom=0;AC_Hemi=0;AN_Adj=2000;AN_KGA=2000;AC_Adj=974;AC_KGA=974;Hom_KGA=0;Het_KGA=974;Hemi_KGA=0;CSQ=A|downstream_gene_variant|MODIFIER|NEK2P2|ENSG00000231565|Transcript|ENST00000438441|processed_pseudogene||||||||||rs371958062|1|4025|1||SNV|HGNC|37816|YES|||||||||||||||||||||||||||||||||||||||||,A|upstream_gene_variant|MODIFIER|LA16c-2F2.8|ENSG00000230471|Transcript|ENST00000428118|lincRNA||||||||||rs371958062|1|2852|1||SNV|Clone_based_vega_gene||YES||||||||||||||||||||||||||||||||||||||||| +22 29461622 rs783 G A 715011 PASS AC=1247;AF=0.624;AN=2000;BaseQRankSum=2.44;ClippingRankSum=-0.031;DB;DP=36991;ExcessHet=4.4124;FS=0;MLEAC=1247;MLEAF=0.624;MQ=60;MQ0=0;MQRankSum=0.023;POSITIVE_TRAIN_SITE;QD=22.28;ReadPosRankSum=0.313;SOR=0.685;VQSLOD=22.38;culprit=MQ;AC_Het=475;AC_Hom=772;AC_Hemi=0;AN_Adj=2000;AN_KGA=2000;AC_Adj=1247;AC_KGA=1247;Hom_KGA=772;Het_KGA=475;Hemi_KGA=0;CSQ=A|upstream_gene_variant|MODIFIER|C22orf31|ENSG00000100249|Transcript|ENST00000216071|protein_coding||||||||||rs783|1|3790|-1||SNV|HGNC|26931|YES|||CCDS13848.1|ENSP00000216071|CV031_HUMAN||UPI0000073FE0||||||G:0.4289|A:0.5681|A:0.4654|A:0.5466|A:0.664|A:0.5798|||||||||||||||||||||||,A|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00001731804|promoter_flanking_region||||||||||rs783|1||||SNV||||||||||||||||G:0.4289|A:0.5681|A:0.4654|A:0.5466|A:0.664|A:0.5798||||||||||||||||||||||| diff --git a/scripts/importer/tests/data/dataset1_2_coverage.txt b/scripts/importer/tests/data/dataset1_2_coverage.txt new file mode 100644 index 000000000..c137bd7b5 --- /dev/null +++ b/scripts/importer/tests/data/dataset1_2_coverage.txt @@ -0,0 +1,24 @@ +#chrom pos mean median 1 5 10 15 20 25 30 50 100 +22 16364820 75.45 71.00 1.0000 1.0000 0.9990 0.9980 0.9980 0.9940 0.9760 0.7930 0.1700 +22 16364830 75.94 71.00 1.0000 1.0000 0.9990 0.9990 0.9980 0.9940 0.9780 0.8020 0.1790 +22 16364840 74.89 70.00 1.0000 1.0000 1.0000 0.9990 0.9970 0.9920 0.9770 0.7920 0.1670 +22 16364850 72.94 69.00 1.0000 1.0000 0.9990 0.9990 0.9970 0.9920 0.9760 0.7720 0.1570 +22 16364860 71.06 67.00 1.0000 1.0000 0.9990 0.9990 0.9970 0.9880 0.9740 0.7620 0.1440 +22 16364870 67.41 63.00 1.0000 1.0000 0.9990 0.9980 0.9970 0.9870 0.9690 0.7220 0.1120 +22 16364880 64.26 60.00 1.0000 1.0000 1.0000 0.9980 0.9940 0.9870 0.9580 0.6930 0.0800 +22 16364890 60.92 58.00 1.0000 1.0000 1.0000 0.9980 0.9950 0.9860 0.9570 0.6370 0.0560 +22 16364900 58.89 56.00 1.0000 1.0000 1.0000 0.9980 0.9950 0.9830 0.9530 0.6120 0.0420 +22 16364910 57.57 54.00 1.0000 1.0000 1.0000 0.9970 0.9940 0.9830 0.9460 0.5900 0.0370 +22 16364920 56.25 53.50 1.0000 1.0000 1.0000 0.9960 0.9910 0.9830 0.9380 0.5710 0.0300 +22 16364930 55.18 53.00 1.0000 1.0000 1.0000 0.9960 0.9910 0.9800 0.9440 0.5470 0.0250 +22 16364940 55.15 53.00 1.0000 1.0000 1.0000 0.9970 0.9910 0.9770 0.9550 0.5560 0.0260 +22 16364950 54.00 52.00 1.0000 1.0000 1.0000 0.9980 0.9910 0.9790 0.9560 0.5320 0.0190 +22 16364960 51.68 50.00 1.0000 1.0000 1.0000 0.9960 0.9900 0.9760 0.9410 0.4760 0.0140 +22 16364970 50.62 48.00 1.0000 1.0000 1.0000 0.9960 0.9890 0.9740 0.9280 0.4510 0.0110 +22 16364980 50.50 48.50 1.0000 1.0000 1.0000 0.9970 0.9900 0.9750 0.9390 0.4510 0.0100 +22 16364990 50.85 49.00 1.0000 1.0000 1.0000 0.9970 0.9930 0.9780 0.9420 0.4600 0.0100 +22 16365000 50.98 49.00 1.0000 1.0000 1.0000 0.9980 0.9920 0.9820 0.9420 0.4540 0.0100 +22 16365010 51.24 49.00 1.0000 1.0000 1.0000 0.9980 0.9920 0.9820 0.9510 0.4520 0.0110 +22 16365020 52.46 50.00 1.0000 1.0000 1.0000 0.9980 0.9920 0.9810 0.9570 0.4890 0.0100 +22 16365030 52.95 51.00 1.0000 1.0000 1.0000 0.9990 0.9930 0.9820 0.9590 0.5050 0.0110 +22 16365040 53.53 51.00 1.0000 1.0000 1.0000 0.9980 0.9950 0.9870 0.9600 0.5210 0.0120 diff --git a/scripts/importer/tests/data/dataset2_1.vcf b/scripts/importer/tests/data/dataset2_1.vcf new file mode 100644 index 000000000..a3d3b9260 --- /dev/null +++ b/scripts/importer/tests/data/dataset2_1.vcf @@ -0,0 +1,265 @@ +##fileformat=VCFv4.1 +##FILTER= +##fileDate=20150218 +##reference=ftp://ftp.1000genomes.ebi.ac.uk//vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz +##source=1000GenomesPhase3Pipeline +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= 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0|1 0|0 1|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|1 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|1 0|0 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|1 0|0 0|0 0|0 0|0 0|0 1|0 0|0 0|0 1|0 0|0 0|0 0|0 0|0 0|0 0|1 0|0 0|0 0|1 0|1 1|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|2 0|0 1|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|2 0|0 0|0 0|0 0|0 0|1 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|1 1|0 0|1 0|0 0|0 0|0 0|1 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|1 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|2 0|0 0|0 0|0 0|1 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 1|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|1 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0 +22 17302972 rs5994030 C A 100 PASS AC=2931;AF=0.585264;AN=5008;NS=2504;DP=14904;EAS_AF=0.5804;AMR_AF=0.6225;AFR_AF=0.6135;EUR_AF=0.5954;SAS_AF=0.5153;AA=.|||;VT=SNP GT 0|0 0|1 0|0 0|1 1|1 1|1 1|0 0|0 0|1 1|0 0|1 1|0 1|1 0|1 1|1 0|0 1|1 1|1 0|0 1|1 1|1 1|0 0|0 0|1 1|0 1|1 1|1 1|1 1|1 0|1 1|0 1|0 1|1 1|1 1|1 1|0 0|0 1|0 1|1 0|0 0|1 1|1 1|1 0|0 1|1 1|0 1|1 1|1 1|1 1|1 1|1 1|1 1|1 0|0 1|1 0|1 1|1 1|1 0|0 1|0 1|0 0|1 0|0 1|1 1|0 0|1 1|1 1|1 0|1 1|1 0|1 1|0 0|0 1|1 1|1 0|0 1|0 0|1 1|0 1|0 1|0 1|1 0|1 0|0 0|1 1|0 1|1 0|1 1|1 1|0 1|0 1|1 1|1 1|0 0|1 0|1 1|1 1|1 1|1 1|1 0|1 1|0 0|1 1|1 1|1 1|0 0|0 1|0 0|0 1|0 1|1 0|0 1|1 1|1 1|1 1|1 1|0 1|0 1|0 1|0 1|1 0|1 1|0 1|1 1|1 1|1 1|0 0|0 1|1 1|0 1|1 0|0 1|0 1|0 1|1 1|0 0|1 1|1 1|0 1|1 1|0 0|0 1|0 1|1 1|0 0|1 1|1 1|1 0|1 1|1 1|0 1|1 1|0 1|0 1|0 1|0 0|1 1|0 1|1 0|1 1|1 1|1 0|1 0|1 0|1 1|0 1|1 1|1 0|0 1|1 1|1 1|1 0|1 0|1 1|1 1|1 1|0 1|1 0|1 1|1 1|0 0|1 0|1 1|1 1|0 1|1 0|1 0|1 1|1 0|0 1|1 0|0 1|0 0|0 0|1 0|0 0|0 0|1 1|1 1|0 1|1 1|1 1|0 1|0 1|1 1|1 0|1 1|0 0|1 1|0 0|0 1|1 1|1 0|1 1|0 0|1 0|1 0|1 1|1 1|1 1|1 1|1 0|1 0|0 0|1 1|0 1|1 1|0 0|1 1|0 1|0 1|0 1|0 0|1 1|0 0|0 0|0 1|0 0|0 1|0 1|1 1|0 1|0 1|1 1|1 0|0 1|1 1|1 1|0 0|1 1|0 0|0 0|1 0|1 0|0 1|1 1|1 0|0 0|1 0|0 1|1 0|1 1|1 0|0 1|1 1|1 1|0 1|0 1|1 0|1 0|1 1|1 1|1 1|0 0|0 0|1 1|0 1|0 0|1 0|0 0|1 1|0 0|1 1|1 1|1 1|0 1|0 0|1 0|1 0|1 1|0 1|0 1|1 1|1 0|0 0|0 1|0 1|1 1|0 0|1 1|1 1|1 1|0 0|0 1|1 0|0 1|1 1|1 1|1 1|1 0|1 1|0 1|0 0|0 1|0 1|0 1|1 1|0 0|1 0|1 1|0 0|1 1|1 1|1 1|0 1|1 1|1 0|1 1|1 0|1 0|1 0|1 0|1 1|1 1|1 1|1 1|0 1|1 0|1 0|0 1|1 0|1 1|1 1|0 1|0 1|0 1|1 0|1 0|1 1|0 1|1 1|1 1|0 1|0 1|1 1|0 1|0 0|0 0|1 0|0 0|1 0|1 1|1 1|1 0|1 1|0 0|1 1|1 1|0 1|1 0|0 0|1 1|1 0|1 1|0 1|0 1|0 1|1 0|1 0|1 0|0 1|0 1|1 0|1 1|1 1|0 0|1 1|0 1|1 0|1 1|0 0|1 1|1 1|0 1|1 1|1 1|1 0|0 1|1 1|1 0|1 0|0 0|1 1|1 0|1 0|1 1|0 0|1 0|1 1|1 1|0 1|1 1|1 0|1 1|1 1|0 1|0 0|1 0|1 1|1 0|1 1|1 0|1 1|1 1|1 1|1 1|1 0|1 0|1 1|1 1|0 1|1 0|0 0|1 1|0 1|1 0|1 1|0 0|1 1|1 0|0 1|1 0|0 0|0 1|0 1|1 1|0 1|0 1|1 0|0 0|0 1|1 0|0 1|0 1|1 1|1 1|1 1|1 1|0 1|0 1|1 1|0 1|0 1|1 1|1 0|0 0|1 1|0 0|0 1|1 0|1 1|1 1|0 0|0 1|0 0|1 1|0 0|0 1|1 1|1 1|0 0|1 0|0 1|0 0|1 1|1 1|1 1|0 0|0 1|1 1|1 0|1 0|1 1|1 1|1 0|1 1|1 1|0 1|1 1|1 0|1 0|1 1|0 1|0 0|1 1|1 1|0 0|1 0|1 0|0 1|0 1|1 0|0 1|1 1|0 0|0 1|0 0|1 1|0 0|0 1|1 1|0 1|0 1|0 1|1 1|1 1|0 0|1 0|0 0|1 1|1 1|0 0|1 0|1 1|1 1|1 0|0 1|0 1|1 1|1 0|1 1|1 1|1 1|0 0|0 0|1 0|1 1|1 1|1 1|1 0|0 0|1 1|0 0|1 1|1 0|0 0|1 1|0 0|0 1|1 1|1 1|1 0|1 0|1 1|0 1|0 1|0 1|0 0|0 1|0 1|0 1|1 0|1 1|0 1|0 1|1 0|1 1|1 1|1 1|1 1|0 1|0 1|0 1|0 0|1 0|0 1|0 0|1 0|0 1|0 1|0 0|1 0|0 1|0 0|0 0|0 0|1 0|0 0|1 0|1 1|1 1|0 0|0 1|1 1|1 1|1 0|1 0|1 0|1 1|0 0|1 1|0 1|1 0|1 0|1 0|1 1|1 1|0 0|0 0|1 1|0 1|1 1|1 1|0 0|0 1|0 1|1 1|1 1|0 1|1 0|1 0|0 0|1 1|0 0|1 1|1 1|0 0|1 0|1 0|1 1|0 0|1 0|1 1|0 1|1 0|0 0|1 1|0 1|1 1|1 1|1 1|1 1|1 1|0 1|0 0|1 1|0 0|1 1|1 1|1 1|1 1|1 0|1 0|1 0|1 1|0 1|1 1|0 1|0 1|1 1|0 1|0 0|1 0|1 1|0 1|1 1|0 1|0 1|1 1|1 0|0 0|0 0|0 0|0 0|1 0|0 1|1 0|1 0|1 1|1 1|1 0|0 1|0 1|1 0|1 1|0 1|1 1|1 1|1 1|1 0|0 1|1 0|0 1|1 0|1 1|1 0|1 1|0 1|1 0|1 0|1 0|1 1|1 0|0 1|1 0|1 1|1 1|1 1|1 0|0 1|1 0|1 1|1 1|0 1|1 1|0 1|1 1|0 0|0 0|1 0|1 1|1 1|1 1|0 0|1 1|0 1|0 0|1 0|0 0|0 1|1 1|1 1|0 1|1 1|0 1|0 0|1 1|0 1|1 0|1 0|1 1|0 1|1 1|1 0|0 0|1 1|0 1|1 1|1 0|1 1|1 1|1 0|1 1|1 1|1 1|0 0|1 1|1 0|0 1|0 0|1 0|1 0|1 1|1 1|1 1|0 1|1 1|0 1|0 0|1 0|0 0|1 0|1 0|0 0|1 1|0 1|1 0|1 0|0 1|1 1|1 1|0 1|0 1|0 0|1 1|1 0|1 1|1 1|1 1|1 1|0 1|0 0|0 1|1 1|1 1|1 1|1 1|1 0|1 1|1 1|0 0|1 0|1 1|1 1|0 1|0 1|1 0|1 1|1 0|0 1|0 0|0 0|1 0|0 0|0 0|1 0|1 0|0 0|0 1|1 0|0 1|0 1|1 0|0 1|1 1|0 1|1 0|0 0|1 1|1 0|1 1|1 0|1 0|0 0|0 1|1 0|0 1|0 0|1 1|1 1|1 1|0 0|1 1|1 1|0 1|1 0|0 0|1 0|1 0|1 1|0 0|1 0|0 0|0 1|1 0|0 0|0 1|1 1|0 0|0 0|0 0|1 0|0 0|1 1|1 1|1 0|1 0|1 0|1 1|1 0|1 1|1 0|0 0|1 0|1 1|1 1|0 1|1 0|1 0|0 0|1 1|1 0|0 1|1 1|1 1|1 1|1 0|0 0|1 1|0 0|0 0|1 0|1 0|0 1|0 1|1 1|1 1|0 0|1 1|1 0|1 1|0 1|0 1|1 0|0 0|1 0|1 1|1 1|1 0|0 1|1 1|1 0|0 1|0 0|0 1|1 0|0 0|1 0|1 1|1 0|1 1|0 1|0 1|0 0|1 1|0 1|0 1|0 1|1 0|0 0|1 1|1 1|0 1|0 0|0 1|1 1|1 1|0 1|1 1|1 0|1 0|0 1|0 0|0 1|1 1|0 0|1 1|1 0|1 1|1 0|1 1|1 1|1 1|1 0|0 0|0 1|0 1|0 0|0 0|1 0|1 1|0 1|1 1|1 1|1 1|0 0|1 0|0 1|1 0|1 1|0 1|1 +22 17300408 rs5748665 A G 100 PASS AC=4723;AF=0.943091;AN=5008;NS=2504;DP=17781;EAS_AF=0.9236;AMR_AF=0.9337;AFR_AF=0.9962;EUR_AF=0.9264;SAS_AF=0.9151;AA=.|||;VT=SNP GT 1|1 1|1 1|0 1|1 1|1 1|1 1|1 1|1 0|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|0 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 0|1 0|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|0 1|1 1|1 1|1 1|1 1|1 1|1 1|1 0|1 0|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|0 1|0 1|1 1|1 1|1 1|1 1|1 1|1 1|0 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 0|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|0 1|1 1|1 0|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|0 1|1 1|0 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 0|1 1|1 1|1 1|1 0|0 1|1 1|1 1|1 1|1 1|1 1|1 1|0 1|1 1|1 1|1 1|0 1|1 1|1 1|1 1|1 1|1 0|1 1|1 1|0 1|1 1|1 1|1 1|1 1|0 1|1 1|1 1|1 1|1 1|1 1|1 0|1 1|1 1|1 1|1 1|1 1|1 0|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 0|1 1|1 1|1 1|1 1|1 1|1 1|1 0|1 1|1 1|0 1|1 1|1 1|1 1|1 1|1 0|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 0|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|0 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|0 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 0|1 1|1 1|1 0|0 1|1 1|0 1|1 1|1 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1|1 1|1 1|1 1|0 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 0|1 1|1 1|1 1|1 1|1 1|0 1|1 0|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 0|1 1|1 1|1 0|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 0|1 1|1 1|1 1|1 1|1 1|1 1|1 0|1 1|1 1|0 1|1 1|1 1|1 1|1 1|1 1|1 1|1 0|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|0 0|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|0 0|1 1|1 1|1 1|1 1|0 1|1 1|0 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|0 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|0 1|1 0|1 1|1 1|1 1|1 1|1 1|1 1|1 0|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|0 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 +22 17301526 rs5844283 ATACATAGTC A 100 PASS AC=2932;AF=0.585463;AN=5008;NS=2504;DP=5287;EAS_AF=0.5804;AMR_AF=0.6225;AFR_AF=0.6135;EUR_AF=0.5954;SAS_AF=0.5164;VT=INDEL GT 0|0 0|1 0|0 0|1 1|1 1|1 1|0 0|0 0|1 1|0 0|1 1|0 1|1 0|1 1|1 0|0 1|1 1|1 0|0 1|1 1|1 1|0 0|0 0|1 1|0 1|1 1|1 1|1 1|1 0|1 1|0 1|0 1|1 1|1 1|1 1|0 0|0 1|0 1|1 0|0 0|1 1|1 1|1 0|0 1|1 1|0 1|1 1|1 1|1 1|1 1|1 1|1 1|1 0|0 1|1 0|1 1|1 1|1 0|0 1|0 1|0 0|1 0|0 1|1 1|0 0|1 1|1 1|1 0|1 1|1 0|1 1|0 0|0 1|1 1|1 0|0 1|0 0|1 1|0 1|0 1|0 1|1 0|1 0|0 0|1 1|0 1|1 0|1 1|1 1|0 1|0 1|1 1|1 1|0 0|1 0|1 1|1 1|1 1|1 1|1 0|1 1|0 0|1 1|1 1|1 1|0 0|0 1|0 0|0 1|0 1|1 0|0 1|1 1|1 1|1 1|1 1|0 1|0 1|0 1|0 1|1 0|1 1|0 1|1 1|1 1|1 1|0 0|0 1|1 1|0 1|1 0|0 1|0 1|0 1|1 1|0 0|1 1|1 1|0 1|1 1|0 0|0 1|0 1|1 1|0 0|1 1|1 1|1 0|1 1|1 1|0 1|1 1|0 1|0 1|0 1|0 0|1 1|0 1|1 0|1 1|1 1|1 0|1 0|1 0|1 1|0 1|1 1|1 0|0 1|1 1|1 1|1 0|1 0|1 1|1 1|1 1|0 1|1 0|1 1|1 1|0 0|1 0|1 1|1 1|0 1|1 0|1 0|1 1|1 0|0 1|1 0|0 1|0 0|0 0|1 0|0 0|0 0|1 1|1 1|0 1|1 1|1 1|0 1|0 1|1 1|1 0|1 1|0 0|1 1|0 0|0 1|1 1|1 0|1 1|0 0|1 0|1 0|1 1|1 1|1 1|1 1|1 0|1 0|0 0|1 1|0 1|1 1|0 0|1 1|0 1|0 1|0 1|0 0|1 1|0 0|0 0|0 1|0 0|0 1|0 1|1 1|0 1|0 1|1 1|1 0|0 1|1 1|1 1|0 0|1 1|0 0|0 0|1 0|1 0|0 1|1 1|1 0|0 0|1 0|0 1|1 0|1 1|1 0|0 1|1 1|1 1|0 1|0 1|1 0|1 0|1 1|1 1|1 1|0 0|0 0|1 1|0 1|0 0|1 0|0 0|1 1|0 0|1 1|1 1|1 1|0 1|0 0|1 0|1 0|1 1|0 1|0 1|1 1|1 0|0 0|0 1|0 1|1 1|0 0|1 1|1 1|1 1|0 0|0 1|1 0|0 1|1 1|1 1|1 1|1 0|1 1|0 1|0 0|0 1|0 1|0 1|1 1|0 0|1 0|1 1|0 0|1 1|1 1|1 1|0 1|1 1|1 0|1 1|1 0|1 0|1 0|1 0|1 1|1 1|1 1|1 1|0 1|1 0|1 0|0 1|1 0|1 1|1 1|0 1|0 1|0 1|1 0|1 0|1 1|0 1|1 1|1 1|0 1|0 1|1 1|0 1|0 0|0 0|1 0|0 0|1 0|1 1|1 1|1 0|1 1|0 0|1 1|1 1|0 1|1 0|0 0|1 1|1 0|1 1|0 1|0 1|0 1|1 0|1 0|1 0|0 1|0 1|1 0|1 1|1 1|0 0|1 1|0 1|1 0|1 1|0 0|1 1|1 1|0 1|1 1|1 1|1 0|0 1|1 1|1 0|1 0|0 0|1 1|1 0|1 0|1 1|0 0|1 0|1 1|1 1|0 1|1 1|1 0|1 1|1 1|0 1|0 0|1 0|1 1|1 0|1 1|1 0|1 1|1 1|1 1|1 1|1 0|1 0|1 1|1 1|0 1|1 0|0 0|1 1|0 1|1 0|1 1|0 0|1 1|1 0|0 1|1 0|0 0|0 1|0 1|1 1|0 1|0 1|1 0|0 0|0 1|1 0|0 1|0 1|1 1|1 1|1 1|1 1|0 1|0 1|1 1|0 1|0 1|1 1|1 0|0 0|1 1|0 0|0 1|1 0|1 1|1 1|0 0|0 1|0 0|1 1|0 0|0 1|1 1|1 1|0 0|1 0|0 1|0 0|1 1|1 1|1 1|0 0|0 1|1 1|1 0|1 0|1 1|1 1|1 0|1 1|1 1|0 1|1 1|1 0|1 0|1 1|0 1|0 0|1 1|1 1|0 0|1 0|1 0|0 1|0 1|1 0|0 1|1 1|0 0|0 1|0 0|1 1|0 0|0 1|1 1|0 1|0 1|0 1|1 1|1 1|0 0|1 0|0 0|1 1|1 1|0 0|1 0|1 1|1 1|1 0|0 1|0 1|1 1|1 0|1 1|1 1|1 1|0 0|0 0|1 0|1 1|1 1|1 1|1 0|0 0|1 1|0 0|1 1|1 0|0 0|1 1|0 0|0 1|1 1|1 1|1 0|1 0|1 1|0 1|0 1|0 1|0 0|0 1|0 1|0 1|1 0|1 1|0 1|0 1|1 0|1 1|1 1|1 1|1 1|0 1|0 1|0 1|0 0|1 0|0 1|0 0|1 0|0 1|0 1|0 0|1 0|0 1|0 0|0 0|0 0|1 0|0 0|1 0|1 1|1 1|0 0|0 1|1 1|1 1|1 0|1 0|1 0|1 1|0 0|1 1|0 1|1 0|1 0|1 0|1 1|1 1|0 0|0 0|1 1|0 1|1 1|1 1|0 0|0 1|0 1|1 1|1 1|0 1|1 0|1 0|0 0|1 1|0 0|1 1|1 1|0 0|1 0|1 0|1 1|0 0|1 0|1 1|0 1|1 0|0 0|1 1|0 1|1 1|1 1|1 1|1 1|1 1|0 1|0 0|1 1|0 0|1 1|1 1|1 1|1 1|1 0|1 0|1 0|1 1|0 1|1 1|0 1|0 1|1 1|0 1|0 0|1 0|1 1|0 1|1 1|0 1|0 1|1 1|1 0|0 0|0 0|0 0|0 0|1 0|0 1|1 0|1 0|1 1|1 1|1 0|0 1|0 1|1 0|1 1|0 1|1 1|1 1|1 1|1 0|0 1|1 0|0 1|1 0|1 1|1 0|1 1|0 1|1 0|1 0|1 0|1 1|1 0|0 1|1 0|1 1|1 1|1 1|1 0|0 1|1 0|1 1|1 1|0 1|1 1|0 1|1 1|0 0|0 0|1 0|1 1|1 1|1 1|0 0|1 1|0 1|0 0|1 0|0 0|0 1|1 1|1 1|0 1|1 1|0 1|0 0|1 1|0 1|1 0|1 0|1 1|0 1|1 1|1 0|0 0|1 1|0 1|1 1|1 0|1 1|1 1|1 0|1 1|1 1|1 1|0 0|1 1|1 0|0 1|0 0|1 0|1 0|1 1|1 1|1 1|0 1|1 1|0 1|0 0|1 0|0 0|1 0|1 0|0 0|1 1|0 1|1 0|1 0|0 1|1 1|1 1|0 1|0 1|0 0|1 1|1 0|1 1|1 1|1 1|1 1|0 1|0 0|0 1|1 1|1 1|1 1|1 1|1 0|1 1|1 1|0 0|1 0|1 1|1 1|0 1|0 1|1 0|1 1|1 0|0 1|0 0|0 0|1 0|0 0|0 0|1 0|1 0|0 0|0 1|1 0|0 1|0 1|1 0|0 1|1 1|0 1|1 0|0 0|1 1|1 0|1 1|1 0|1 0|0 0|0 1|1 0|0 1|0 0|1 1|1 1|1 1|0 0|1 1|1 1|0 1|1 0|0 0|1 0|1 0|1 1|0 0|1 0|0 0|0 1|1 0|0 0|0 1|1 1|0 0|0 0|0 0|1 0|0 0|1 1|1 1|1 0|1 0|1 0|1 1|1 0|1 1|1 0|0 0|1 0|1 1|1 1|0 1|1 0|1 0|0 0|1 1|1 0|0 1|1 1|1 1|1 1|1 0|0 0|1 1|0 0|0 0|1 0|1 0|0 1|0 1|1 1|1 1|0 0|1 1|1 0|1 1|0 1|0 1|1 0|0 0|1 0|1 1|1 1|1 0|0 1|1 1|1 0|0 1|0 0|0 1|1 0|0 0|1 0|1 1|1 0|1 1|0 1|0 1|0 0|1 1|0 1|0 1|0 1|1 0|0 0|1 1|1 1|0 1|0 0|0 1|1 1|1 1|0 1|1 1|1 0|1 0|0 1|0 0|0 1|1 1|0 0|1 1|1 0|1 1|1 0|1 1|1 1|1 1|1 0|0 0|0 1|0 1|0 0|0 0|1 0|1 1|0 1|1 1|1 1|1 1|0 0|1 0|0 1|1 0|1 1|0 1 +22 19617927 rs553611103;rs553611103;rs148427666 GTCT GTCTTCT,GTCTTCTTCT,G 100 PASS AC=118,17,182;AF=0.0235623,0.00339457,0.0363419;AN=5008;NS=2504;DP=24087;EAS_AF=0.0109,0,0.0873;AMR_AF=0.0461,0.0014,0.0231;AFR_AF=0.0182,0.0121,0.0098;EUR_AF=0.0268,0,0.0447;SAS_AF=0.0245,0,0.0204;VT=INDEL;MULTI_ALLELIC GT 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|1 0|0 0|0 0|0 0|0 0|0 0|3 0|3 3|0 0|0 1|0 0|0 1|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 3|0 0|0 0|0 0|0 0|0 0|0 0|1 0|0 0|0 0|0 0|0 3|3 0|0 3|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 3|0 0|0 0|3 0|0 0|0 0|0 0|0 0|0 0|3 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|3 0|0 0|0 0|0 0|0 3|0 0|3 0|0 0|0 0|0 0|0 0|0 3|0 0|0 0|0 0|0 1|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|3 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|1 0|0 1|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|3 0|0 0|1 0|0 0|0 0|0 0|0 0|0 0|0 3|0 0|0 0|0 0|0 0|0 0|0 3|0 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0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 2|0 2|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|2 0|0 0|0 0|0 0|0 0|0 0|0 diff --git a/scripts/importer/tests/data/dbNSFP_gene.txt b/scripts/importer/tests/data/dbNSFP_gene.txt new file mode 100644 index 000000000..66967f047 --- /dev/null +++ b/scripts/importer/tests/data/dbNSFP_gene.txt @@ -0,0 +1,5 @@ +Gene_name Ensembl_gene chr Gene_old_names Gene_other_names Uniprot_acc Uniprot_id Entrez_gene_id CCDS_id Refseq_id ucsc_id MIM_id Gene_full_name Pathway(BioCarta)_short Pathway(BioCarta)_full Pathway(ConsensusPathDB) Pathway(KEGG)_id Pathway(KEGG)_full Function_description Disease_description MIM_phenotype_id MIM_disease Trait_association(GWAS) GO_Slim_biological_process GO_Slim_cellular_component GO_Slim_molecular_function Expression(egenetics) Expression(GNF/Atlas) Interactions(IntAct) Interactions(BioGRID) Interactions(ConsensusPathDB) P(HI) P(rec) Known_rec_info Essential_gene MGI_mouse_gene MGI_mouse_phenotype ZFIN_zebrafish_gene ZFIN_zebrafish_structure ZFIN_zebrafish_phenotype_quality ZFIN_zebrafish_phenotype_tag +BCL2L13 ENSG00000099968 22 . MIL1;BCL-RAMBO Q9BXK5 B2L13_HUMAN 23786 CCDS13746.1;CCDS59447.1;CCDS59448.1 NM_015367;NM_001270727 uc002zmw.4 . BCL2-like 13 (apoptosis facilitator) . . Legionellosis - Homo sapiens (human) . . May promote the activation of caspase-3 and apoptosis. . . . . cell death cellular_component;nucleus;mitochondrion enzyme regulator activity;peptidase activity medulla oblongata;smooth muscle;skin;bone marrow;retina;prostate;optic nerve;frontal lobe;endometrium;thyroid;iris;germinal center;bladder;brain;heart;cartilage;tongue;blood;lens;skeletal muscle;breast;macula lutea;visual apparatus;liver;alveolus;cervix;spleen;mammary gland;colon;parathyroid;fovea centralis;choroid;uterus;whole body;bone;pituitary gland;testis;unclassifiable (Anatomical System);lymph node;trophoblast;islets of Langerhans;bile duct;pancreas;lung;nasopharynx;placenta;duodenum;head and neck;kidney;stomach;thymus;cerebellum; testis; 3 2 3 0.05910 . . . Bcl2l13 . . . . . +BID ENSG00000015475 22 . . P55957 BID_HUMAN 637 CCDS13747.1;CCDS13748.1;CCDS13749.1 NM_197966;XR_244338 uc002znc.2 601997 BH3 interacting domain death agonist chemicalPathway;HivnefPathway;deathPathway;mitochondriaPathway Apoptotic Signaling in Response to DNA Damage;HIV-I Nef: negative effector of Fas and TNF;Induction of apoptosis through DR3 and DR4/5 Death Receptors ;Role of Mitochondria in Apoptotic Signaling miRNA Regulation of DNA Damage Response;TP53 Network;Apoptosis Modulation and Signaling;Intrinsic Pathway for Apoptosis;Amyotrophic lateral sclerosis (ALS);ATM Signaling Pathway;Apoptosis;Apoptosis Modulation by HSP70;Integrated Breast Cancer Pathway;Alzheimers Disease;TNF alpha Signaling Pathway;Integrated Pancreatic Cancer Pathway;DNA Damage Response;Viral myocarditis - Homo sapiens (human);Alzheimer,s disease - Homo sapiens (human);Amyotrophic lateral sclerosis (ALS) - Homo sapiens (human);p53 signaling pathway - Homo sapiens (human);Tuberculosis - Homo sapiens (human);Natural killer cell mediated cytotoxicity - Homo sapiens (human);Pathways in cancer - Homo sapiens (human);Apoptosis - Homo sapiens (human);Direct p53 effectors;induction of apoptosis through dr3 and dr4/5 death receptors;Caspase Cascade in Apoptosis;Activation of BAD and translocation to mitochondria;Fas;TNF;TNFalpha;BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members;induction of apoptosis through dr3 and dr4/5 death receptors;Ceramide signaling pathway;FAS (CD95) signaling pathway;HIV-1 Nef: Negative effector of Fas and TNF-alpha;Intrinsic Pathway for Apoptosis;apoptotic signaling in response to dna damage;ATM pathway;Activation and oligomerization of BAK protein;hiv-1 nef: negative effector of fas and tnf;Activation, translocation and oligomerization of BAX;role of mitochondria in apoptotic signaling;Activation, myristolyation of BID and translocation to mitochondria;apoptotic signaling in response to dna damage;role of mitochondria in apoptotic signaling;hiv-1 nef: negative effector of fas and tnf;Activation, myristolyation of BID and translocation to mitochondria;Activation and oligomerization of BAK protein;Activation of BAD and translocation to mitochondria ;Activation of BH3-only proteins;BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members;Activation, translocation and oligomerization of BAX;Intrinsic Pathway for Apoptosis;Apoptosis hsa04115;hsa04210;hsa04650 p53 signaling pathway;Apoptosis;Natural killer cell mediated cytotoxicity The major proteolytic product p15 BID allows the release of cytochrome c (By similarity). Isoform 1, isoform 2 and isoform 4 induce ICE-like proteases and apoptosis. Isoform 3 does not induce apoptosis. Counters the protective effect of Bcl-2. . . . . membrane organization;mitochondrion organization;protein complex assembly;anatomical structure development;biological_process;protein targeting;cell proliferation;cell death;cell cycle;signal transduction;transport mitochondrion;cellular_component;cytosol enzyme binding;molecular_function myocardium;ovary;salivary gland;colon;parathyroid;fovea centralis;choroid;vein;skin;retina;uterus;prostate;optic nerve;whole body;frontal lobe;endometrium;bone;testis;germinal center;brain;unclassifiable (Anatomical System);lymph node;cartilage;heart;islets of Langerhans;lens;skeletal muscle;breast;pancreas;lung;placenta;macula lutea;visual apparatus;liver;spleen;cervix;kidney;stomach; whole brain;liver;globus pallidus;white blood cells;whole blood;trigeminal ganglion; 24 42 72 0.06027 0.11574 lof-tolerant N Bid cellular phenotype; homeostasis/metabolism phenotype; muscle phenotype; endocrine/exocrine gland phenotype; mortality/aging (characteristics involving the ability of an organism to live and age normally throughout development and life span); hematopoietic system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); respiratory system phenotype; liver/biliary system phenotype; immune system phenotype; vision/eye phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); . . . . +NEK2P2 ENSG00000231565 22 . . . . 100379667 . NG_016726 . . NEK2 pseudogene 2 . . . . . . . . . . . . . . . 1 1 1 . . . . . . . . . . +POTEH ENSG00000198062 22 ACTBL1;A26C3 POTE22;CT104.7 Q6S545 POTEH_HUMAN 23784 CCDS46658.1 NM_001136213 uc010gqp.2 608913 POTE ankyrin domain family, member H . . . . . . . . . . . . . prostate;testis;stomach; . 1 1 1 0.04666 0.08864 . . . . . . . . diff --git a/scripts/importer/tests/data/gencode.gtf b/scripts/importer/tests/data/gencode.gtf new file mode 100644 index 000000000..d1aaf3e27 --- /dev/null +++ b/scripts/importer/tests/data/gencode.gtf @@ -0,0 +1,374 @@ +chr22 HAVANA gene 16256441 16287937 . - . gene_id "ENSG00000198062.10"; transcript_id "ENSG00000198062.10"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "POTEH"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "POTEH"; level 1; tag "ncRNA_host"; havana_gene "OTTHUMG00000140314.5"; +chr22 HAVANA transcript 16256441 16287717 . - . gene_id "ENSG00000198062.10"; transcript_id "ENST00000452800.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "POTEH"; transcript_type "nonsense_mediated_decay"; transcript_status "KNOWN"; transcript_name "POTEH-002"; level 2; protein_id "ENSP00000442107.1"; tag "mRNA_start_NF"; tag "cds_start_NF"; havana_gene "OTTHUMG00000140314.5"; havana_transcript "OTTHUMT00000340296.2"; +chr22 HAVANA exon 16287254 16287717 . - . gene_id "ENSG00000198062.10"; transcript_id "ENST00000452800.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "POTEH"; transcript_type "nonsense_mediated_decay"; transcript_status "KNOWN"; transcript_name "POTEH-002"; exon_number 1; exon_id "ENSE00001781695.1"; level 2; protein_id "ENSP00000442107.1"; tag "mRNA_start_NF"; tag "cds_start_NF"; havana_gene "OTTHUMG00000140314.5"; havana_transcript "OTTHUMT00000340296.2"; +chr22 HAVANA CDS 16287254 16287717 . - 0 gene_id "ENSG00000198062.10"; transcript_id "ENST00000452800.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "POTEH"; transcript_type "nonsense_mediated_decay"; transcript_status "KNOWN"; transcript_name "POTEH-002"; exon_number 1; exon_id "ENSE00001781695.1"; level 2; protein_id "ENSP00000442107.1"; tag "mRNA_start_NF"; tag "cds_start_NF"; havana_gene "OTTHUMG00000140314.5"; havana_transcript "OTTHUMT00000340296.2"; +chr22 HAVANA exon 16282478 16282592 . - . gene_id "ENSG00000198062.10"; transcript_id "ENST00000452800.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "POTEH"; transcript_type "nonsense_mediated_decay"; transcript_status "KNOWN"; transcript_name "POTEH-002"; exon_number 2; exon_id "ENSE00001746577.1"; level 2; protein_id "ENSP00000442107.1"; tag "mRNA_start_NF"; tag "cds_start_NF"; havana_gene "OTTHUMG00000140314.5"; havana_transcript "OTTHUMT00000340296.2"; +chr22 HAVANA CDS 16282478 16282592 . - 1 gene_id "ENSG00000198062.10"; transcript_id "ENST00000452800.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "POTEH"; transcript_type "nonsense_mediated_decay"; transcript_status "KNOWN"; transcript_name "POTEH-002"; exon_number 2; exon_id "ENSE00001746577.1"; level 2; protein_id "ENSP00000442107.1"; tag "mRNA_start_NF"; tag "cds_start_NF"; havana_gene "OTTHUMG00000140314.5"; havana_transcript "OTTHUMT00000340296.2"; +chr22 HAVANA exon 16282145 16282318 . - . gene_id "ENSG00000198062.10"; transcript_id "ENST00000452800.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "POTEH"; transcript_type "nonsense_mediated_decay"; transcript_status "KNOWN"; transcript_name "POTEH-002"; exon_number 3; exon_id "ENSE00001788239.1"; level 2; protein_id "ENSP00000442107.1"; tag "mRNA_start_NF"; tag "cds_start_NF"; havana_gene "OTTHUMG00000140314.5"; havana_transcript "OTTHUMT00000340296.2"; +chr22 HAVANA CDS 16282145 16282318 . - 0 gene_id "ENSG00000198062.10"; transcript_id "ENST00000452800.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "POTEH"; transcript_type "nonsense_mediated_decay"; transcript_status "KNOWN"; transcript_name "POTEH-002"; exon_number 3; exon_id "ENSE00001788239.1"; level 2; protein_id "ENSP00000442107.1"; tag "mRNA_start_NF"; tag "cds_start_NF"; havana_gene "OTTHUMG00000140314.5"; havana_transcript "OTTHUMT00000340296.2"; +chr22 HAVANA exon 16280334 16280589 . - . gene_id "ENSG00000198062.10"; transcript_id "ENST00000452800.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "POTEH"; transcript_type "nonsense_mediated_decay"; transcript_status "KNOWN"; transcript_name "POTEH-002"; exon_number 4; exon_id "ENSE00001593346.1"; level 2; protein_id "ENSP00000442107.1"; tag "mRNA_start_NF"; tag "cds_start_NF"; havana_gene "OTTHUMG00000140314.5"; havana_transcript "OTTHUMT00000340296.2"; +chr22 HAVANA CDS 16280434 16280589 . - 0 gene_id "ENSG00000198062.10"; transcript_id "ENST00000452800.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "POTEH"; transcript_type "nonsense_mediated_decay"; transcript_status "KNOWN"; transcript_name "POTEH-002"; exon_number 4; exon_id "ENSE00001593346.1"; level 2; protein_id "ENSP00000442107.1"; tag "mRNA_start_NF"; tag "cds_start_NF"; havana_gene "OTTHUMG00000140314.5"; havana_transcript "OTTHUMT00000340296.2"; +chr22 HAVANA stop_codon 16280431 16280433 . - 0 gene_id "ENSG00000198062.10"; transcript_id "ENST00000452800.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "POTEH"; transcript_type "nonsense_mediated_decay"; transcript_status "KNOWN"; transcript_name "POTEH-002"; exon_number 4; exon_id "ENSE00001593346.1"; level 2; protein_id "ENSP00000442107.1"; tag "mRNA_start_NF"; tag "cds_start_NF"; havana_gene "OTTHUMG00000140314.5"; havana_transcript "OTTHUMT00000340296.2"; +chr22 HAVANA exon 16279195 16279301 . - . gene_id "ENSG00000198062.10"; transcript_id "ENST00000452800.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "POTEH"; transcript_type "nonsense_mediated_decay"; transcript_status "KNOWN"; transcript_name "POTEH-002"; exon_number 5; exon_id "ENSE00003460670.1"; level 2; protein_id "ENSP00000442107.1"; tag "mRNA_start_NF"; tag "cds_start_NF"; havana_gene "OTTHUMG00000140314.5"; havana_transcript "OTTHUMT00000340296.2"; +chr22 HAVANA exon 16277748 16277885 . - . gene_id "ENSG00000198062.10"; transcript_id "ENST00000452800.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "POTEH"; transcript_type "nonsense_mediated_decay"; transcript_status "KNOWN"; transcript_name "POTEH-002"; exon_number 6; exon_id "ENSE00003669720.1"; level 2; protein_id "ENSP00000442107.1"; tag "mRNA_start_NF"; tag "cds_start_NF"; havana_gene "OTTHUMG00000140314.5"; havana_transcript "OTTHUMT00000340296.2"; +chr22 HAVANA exon 16275207 16275277 . - . gene_id "ENSG00000198062.10"; transcript_id "ENST00000452800.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "POTEH"; transcript_type "nonsense_mediated_decay"; transcript_status "KNOWN"; transcript_name "POTEH-002"; exon_number 7; exon_id "ENSE00003508115.1"; level 2; protein_id "ENSP00000442107.1"; tag "mRNA_start_NF"; tag "cds_start_NF"; havana_gene "OTTHUMG00000140314.5"; havana_transcript "OTTHUMT00000340296.2"; +chr22 HAVANA exon 16269873 16269943 . - . gene_id "ENSG00000198062.10"; transcript_id "ENST00000452800.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "POTEH"; transcript_type "nonsense_mediated_decay"; transcript_status "KNOWN"; transcript_name "POTEH-002"; exon_number 8; exon_id "ENSE00003515936.1"; level 2; protein_id "ENSP00000442107.1"; tag "mRNA_start_NF"; tag "cds_start_NF"; havana_gene "OTTHUMG00000140314.5"; havana_transcript "OTTHUMT00000340296.2"; +chr22 HAVANA exon 16268137 16268181 . - . gene_id "ENSG00000198062.10"; transcript_id "ENST00000452800.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "POTEH"; transcript_type "nonsense_mediated_decay"; transcript_status "KNOWN"; transcript_name "POTEH-002"; exon_number 9; exon_id "ENSE00003572616.1"; level 2; protein_id "ENSP00000442107.1"; tag "mRNA_start_NF"; tag "cds_start_NF"; havana_gene "OTTHUMG00000140314.5"; havana_transcript "OTTHUMT00000340296.2"; +chr22 HAVANA exon 16266929 16267095 . - . gene_id "ENSG00000198062.10"; transcript_id "ENST00000452800.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "POTEH"; transcript_type "nonsense_mediated_decay"; transcript_status "KNOWN"; transcript_name "POTEH-002"; exon_number 10; exon_id "ENSE00003639659.1"; level 2; protein_id "ENSP00000442107.1"; tag "mRNA_start_NF"; tag "cds_start_NF"; havana_gene "OTTHUMG00000140314.5"; havana_transcript "OTTHUMT00000340296.2"; +chr22 HAVANA exon 16258185 16258303 . - . gene_id "ENSG00000198062.10"; transcript_id "ENST00000452800.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "POTEH"; transcript_type "nonsense_mediated_decay"; transcript_status "KNOWN"; transcript_name "POTEH-002"; exon_number 11; exon_id "ENSE00003480843.1"; level 2; protein_id "ENSP00000442107.1"; tag "mRNA_start_NF"; tag "cds_start_NF"; havana_gene "OTTHUMG00000140314.5"; havana_transcript "OTTHUMT00000340296.2"; +chr22 HAVANA exon 16256441 16256677 . - . gene_id "ENSG00000198062.10"; transcript_id "ENST00000452800.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "POTEH"; transcript_type "nonsense_mediated_decay"; transcript_status "KNOWN"; transcript_name "POTEH-002"; exon_number 12; exon_id "ENSE00001732273.1"; level 2; protein_id "ENSP00000442107.1"; tag "mRNA_start_NF"; tag "cds_start_NF"; havana_gene "OTTHUMG00000140314.5"; havana_transcript "OTTHUMT00000340296.2"; +chr22 HAVANA UTR 16280334 16280433 . - . gene_id "ENSG00000198062.10"; transcript_id "ENST00000452800.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "POTEH"; transcript_type "nonsense_mediated_decay"; transcript_status "KNOWN"; transcript_name "POTEH-002"; level 2; protein_id "ENSP00000442107.1"; tag "mRNA_start_NF"; tag "cds_start_NF"; havana_gene "OTTHUMG00000140314.5"; havana_transcript "OTTHUMT00000340296.2"; +chr22 HAVANA UTR 16279195 16279301 . - . gene_id "ENSG00000198062.10"; transcript_id "ENST00000452800.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "POTEH"; transcript_type "nonsense_mediated_decay"; transcript_status "KNOWN"; transcript_name "POTEH-002"; level 2; protein_id "ENSP00000442107.1"; tag "mRNA_start_NF"; tag "cds_start_NF"; havana_gene "OTTHUMG00000140314.5"; havana_transcript "OTTHUMT00000340296.2"; +chr22 HAVANA UTR 16277748 16277885 . - . gene_id "ENSG00000198062.10"; transcript_id "ENST00000452800.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "POTEH"; transcript_type "nonsense_mediated_decay"; transcript_status "KNOWN"; transcript_name "POTEH-002"; level 2; protein_id "ENSP00000442107.1"; tag "mRNA_start_NF"; tag "cds_start_NF"; havana_gene "OTTHUMG00000140314.5"; havana_transcript "OTTHUMT00000340296.2"; +chr22 HAVANA UTR 16275207 16275277 . - . gene_id "ENSG00000198062.10"; transcript_id "ENST00000452800.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "POTEH"; transcript_type "nonsense_mediated_decay"; transcript_status "KNOWN"; transcript_name "POTEH-002"; level 2; protein_id "ENSP00000442107.1"; tag "mRNA_start_NF"; tag "cds_start_NF"; havana_gene "OTTHUMG00000140314.5"; havana_transcript "OTTHUMT00000340296.2"; +chr22 HAVANA UTR 16269873 16269943 . - . gene_id "ENSG00000198062.10"; transcript_id "ENST00000452800.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "POTEH"; transcript_type "nonsense_mediated_decay"; transcript_status "KNOWN"; transcript_name "POTEH-002"; level 2; protein_id "ENSP00000442107.1"; tag "mRNA_start_NF"; tag "cds_start_NF"; havana_gene "OTTHUMG00000140314.5"; havana_transcript "OTTHUMT00000340296.2"; +chr22 HAVANA UTR 16268137 16268181 . - . gene_id "ENSG00000198062.10"; transcript_id "ENST00000452800.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "POTEH"; transcript_type "nonsense_mediated_decay"; transcript_status "KNOWN"; transcript_name "POTEH-002"; level 2; protein_id "ENSP00000442107.1"; tag "mRNA_start_NF"; tag "cds_start_NF"; havana_gene "OTTHUMG00000140314.5"; havana_transcript "OTTHUMT00000340296.2"; +chr22 HAVANA UTR 16266929 16267095 . - . gene_id "ENSG00000198062.10"; transcript_id "ENST00000452800.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "POTEH"; transcript_type "nonsense_mediated_decay"; transcript_status "KNOWN"; transcript_name "POTEH-002"; level 2; protein_id "ENSP00000442107.1"; tag "mRNA_start_NF"; tag "cds_start_NF"; havana_gene "OTTHUMG00000140314.5"; havana_transcript "OTTHUMT00000340296.2"; +chr22 HAVANA UTR 16258185 16258303 . - . gene_id "ENSG00000198062.10"; transcript_id "ENST00000452800.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "POTEH"; transcript_type "nonsense_mediated_decay"; transcript_status "KNOWN"; transcript_name "POTEH-002"; level 2; protein_id "ENSP00000442107.1"; tag "mRNA_start_NF"; tag "cds_start_NF"; havana_gene "OTTHUMG00000140314.5"; havana_transcript "OTTHUMT00000340296.2"; +chr22 HAVANA UTR 16256441 16256677 . - . gene_id "ENSG00000198062.10"; transcript_id "ENST00000452800.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "POTEH"; transcript_type "nonsense_mediated_decay"; transcript_status "KNOWN"; transcript_name "POTEH-002"; level 2; protein_id "ENSP00000442107.1"; tag "mRNA_start_NF"; tag "cds_start_NF"; havana_gene "OTTHUMG00000140314.5"; havana_transcript "OTTHUMT00000340296.2"; +chr22 HAVANA transcript 16256441 16287937 . - . gene_id "ENSG00000198062.10"; transcript_id "ENST00000343518.6"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "POTEH"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "POTEH-001"; level 1; protein_id "ENSP00000340610.6"; tag "basic"; tag "appris_principal"; tag "exp_conf"; tag "CCDS"; ccdsid "CCDS46658.1"; havana_gene "OTTHUMG00000140314.5"; havana_transcript "OTTHUMT00000276918.4"; +chr22 HAVANA exon 16287254 16287937 . - . gene_id "ENSG00000198062.10"; transcript_id "ENST00000343518.6"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "POTEH"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "POTEH-001"; exon_number 1; exon_id "ENSE00001413705.2"; level 1; protein_id "ENSP00000340610.6"; tag "basic"; tag "appris_principal"; tag "exp_conf"; tag "CCDS"; ccdsid "CCDS46658.1"; havana_gene "OTTHUMG00000140314.5"; havana_transcript "OTTHUMT00000276918.4"; +chr22 HAVANA CDS 16287254 16287885 . - 0 gene_id "ENSG00000198062.10"; transcript_id "ENST00000343518.6"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "POTEH"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "POTEH-001"; exon_number 1; exon_id "ENSE00001413705.2"; level 1; protein_id "ENSP00000340610.6"; tag "basic"; tag "appris_principal"; tag "exp_conf"; tag "CCDS"; ccdsid "CCDS46658.1"; havana_gene "OTTHUMG00000140314.5"; havana_transcript "OTTHUMT00000276918.4"; +chr22 HAVANA start_codon 16287883 16287885 . - 0 gene_id "ENSG00000198062.10"; transcript_id "ENST00000343518.6"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "POTEH"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "POTEH-001"; exon_number 1; exon_id "ENSE00001413705.2"; level 1; protein_id "ENSP00000340610.6"; tag "basic"; tag "appris_principal"; tag "exp_conf"; tag "CCDS"; ccdsid "CCDS46658.1"; havana_gene "OTTHUMG00000140314.5"; havana_transcript "OTTHUMT00000276918.4"; +chr22 HAVANA exon 16282478 16282592 . - . gene_id "ENSG00000198062.10"; transcript_id "ENST00000343518.6"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "POTEH"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "POTEH-001"; exon_number 2; exon_id "ENSE00001746577.1"; level 1; protein_id "ENSP00000340610.6"; tag "basic"; tag "appris_principal"; tag "exp_conf"; tag "CCDS"; ccdsid "CCDS46658.1"; havana_gene "OTTHUMG00000140314.5"; havana_transcript "OTTHUMT00000276918.4"; +chr22 HAVANA CDS 16282478 16282592 . - 1 gene_id "ENSG00000198062.10"; transcript_id "ENST00000343518.6"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "POTEH"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "POTEH-001"; exon_number 2; exon_id "ENSE00001746577.1"; level 1; protein_id "ENSP00000340610.6"; tag "basic"; tag "appris_principal"; tag "exp_conf"; tag "CCDS"; ccdsid "CCDS46658.1"; havana_gene "OTTHUMG00000140314.5"; havana_transcript "OTTHUMT00000276918.4"; +chr22 HAVANA exon 16282145 16282318 . - . gene_id "ENSG00000198062.10"; transcript_id "ENST00000343518.6"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "POTEH"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "POTEH-001"; exon_number 3; exon_id "ENSE00001788239.1"; level 1; protein_id "ENSP00000340610.6"; tag "basic"; tag "appris_principal"; tag "exp_conf"; tag "CCDS"; ccdsid "CCDS46658.1"; havana_gene "OTTHUMG00000140314.5"; havana_transcript "OTTHUMT00000276918.4"; +chr22 HAVANA CDS 16282145 16282318 . - 0 gene_id "ENSG00000198062.10"; transcript_id "ENST00000343518.6"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "POTEH"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "POTEH-001"; exon_number 3; exon_id "ENSE00001788239.1"; level 1; protein_id "ENSP00000340610.6"; tag "basic"; tag "appris_principal"; tag "exp_conf"; tag "CCDS"; ccdsid "CCDS46658.1"; havana_gene "OTTHUMG00000140314.5"; havana_transcript "OTTHUMT00000276918.4"; +chr22 HAVANA exon 16279195 16279301 . - . gene_id "ENSG00000198062.10"; transcript_id "ENST00000343518.6"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "POTEH"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "POTEH-001"; exon_number 4; exon_id "ENSE00003639359.1"; level 1; protein_id "ENSP00000340610.6"; tag "basic"; tag "appris_principal"; tag "exp_conf"; tag "CCDS"; ccdsid "CCDS46658.1"; havana_gene "OTTHUMG00000140314.5"; havana_transcript "OTTHUMT00000276918.4"; +chr22 HAVANA CDS 16279195 16279301 . - 0 gene_id "ENSG00000198062.10"; transcript_id "ENST00000343518.6"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "POTEH"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "POTEH-001"; exon_number 4; exon_id "ENSE00003639359.1"; level 1; protein_id "ENSP00000340610.6"; tag "basic"; tag "appris_principal"; tag "exp_conf"; tag "CCDS"; ccdsid "CCDS46658.1"; havana_gene "OTTHUMG00000140314.5"; havana_transcript "OTTHUMT00000276918.4"; +chr22 HAVANA exon 16277748 16277885 . - . gene_id "ENSG00000198062.10"; transcript_id "ENST00000343518.6"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "POTEH"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "POTEH-001"; exon_number 5; exon_id "ENSE00003623625.1"; level 1; protein_id "ENSP00000340610.6"; tag "basic"; tag "appris_principal"; tag "exp_conf"; tag "CCDS"; ccdsid "CCDS46658.1"; havana_gene "OTTHUMG00000140314.5"; havana_transcript "OTTHUMT00000276918.4"; +chr22 HAVANA CDS 16277748 16277885 . - 1 gene_id "ENSG00000198062.10"; transcript_id "ENST00000343518.6"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "POTEH"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "POTEH-001"; exon_number 5; exon_id "ENSE00003623625.1"; level 1; protein_id "ENSP00000340610.6"; tag "basic"; tag "appris_principal"; tag "exp_conf"; tag "CCDS"; ccdsid "CCDS46658.1"; havana_gene "OTTHUMG00000140314.5"; havana_transcript "OTTHUMT00000276918.4"; +chr22 HAVANA exon 16275207 16275277 . - . gene_id "ENSG00000198062.10"; transcript_id "ENST00000343518.6"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "POTEH"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "POTEH-001"; exon_number 6; exon_id "ENSE00003533849.1"; level 1; protein_id "ENSP00000340610.6"; tag "basic"; tag "appris_principal"; tag "exp_conf"; tag "CCDS"; ccdsid "CCDS46658.1"; havana_gene "OTTHUMG00000140314.5"; havana_transcript "OTTHUMT00000276918.4"; +chr22 HAVANA CDS 16275207 16275277 . - 1 gene_id "ENSG00000198062.10"; transcript_id "ENST00000343518.6"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "POTEH"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "POTEH-001"; exon_number 6; exon_id "ENSE00003533849.1"; level 1; protein_id "ENSP00000340610.6"; tag "basic"; tag "appris_principal"; tag "exp_conf"; tag "CCDS"; ccdsid "CCDS46658.1"; havana_gene "OTTHUMG00000140314.5"; havana_transcript "OTTHUMT00000276918.4"; +chr22 HAVANA exon 16269873 16269943 . - . gene_id "ENSG00000198062.10"; transcript_id "ENST00000343518.6"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "POTEH"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "POTEH-001"; exon_number 7; exon_id "ENSE00003535920.1"; level 1; protein_id "ENSP00000340610.6"; tag "basic"; tag "appris_principal"; tag "exp_conf"; tag "CCDS"; ccdsid "CCDS46658.1"; havana_gene "OTTHUMG00000140314.5"; havana_transcript "OTTHUMT00000276918.4"; +chr22 HAVANA CDS 16269873 16269943 . - 2 gene_id "ENSG00000198062.10"; transcript_id "ENST00000343518.6"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "POTEH"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "POTEH-001"; exon_number 7; exon_id "ENSE00003535920.1"; level 1; protein_id "ENSP00000340610.6"; tag "basic"; tag "appris_principal"; tag "exp_conf"; tag "CCDS"; ccdsid "CCDS46658.1"; havana_gene "OTTHUMG00000140314.5"; havana_transcript "OTTHUMT00000276918.4"; +chr22 HAVANA exon 16268137 16268181 . - . gene_id "ENSG00000198062.10"; transcript_id "ENST00000343518.6"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "POTEH"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "POTEH-001"; exon_number 8; exon_id "ENSE00003539333.1"; level 1; protein_id "ENSP00000340610.6"; tag "basic"; tag "appris_principal"; tag "exp_conf"; tag "CCDS"; ccdsid "CCDS46658.1"; havana_gene "OTTHUMG00000140314.5"; havana_transcript "OTTHUMT00000276918.4"; +chr22 HAVANA CDS 16268137 16268181 . - 0 gene_id "ENSG00000198062.10"; transcript_id "ENST00000343518.6"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "POTEH"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "POTEH-001"; exon_number 8; exon_id "ENSE00003539333.1"; level 1; protein_id "ENSP00000340610.6"; tag "basic"; tag "appris_principal"; tag "exp_conf"; tag "CCDS"; ccdsid "CCDS46658.1"; havana_gene "OTTHUMG00000140314.5"; havana_transcript "OTTHUMT00000276918.4"; +chr22 HAVANA exon 16266929 16267095 . - . gene_id "ENSG00000198062.10"; transcript_id "ENST00000343518.6"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "POTEH"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "POTEH-001"; exon_number 9; exon_id "ENSE00003523951.1"; level 1; protein_id "ENSP00000340610.6"; tag "basic"; tag "appris_principal"; tag "exp_conf"; tag "CCDS"; ccdsid "CCDS46658.1"; havana_gene "OTTHUMG00000140314.5"; havana_transcript "OTTHUMT00000276918.4"; +chr22 HAVANA CDS 16266929 16267095 . - 0 gene_id "ENSG00000198062.10"; transcript_id "ENST00000343518.6"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "POTEH"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "POTEH-001"; exon_number 9; exon_id "ENSE00003523951.1"; level 1; protein_id "ENSP00000340610.6"; tag "basic"; tag "appris_principal"; tag "exp_conf"; tag "CCDS"; ccdsid "CCDS46658.1"; havana_gene "OTTHUMG00000140314.5"; havana_transcript "OTTHUMT00000276918.4"; +chr22 HAVANA exon 16258185 16258303 . - . gene_id "ENSG00000198062.10"; transcript_id "ENST00000343518.6"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "POTEH"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "POTEH-001"; exon_number 10; exon_id "ENSE00003563151.1"; level 1; protein_id "ENSP00000340610.6"; tag "basic"; tag "appris_principal"; tag "exp_conf"; tag "CCDS"; ccdsid "CCDS46658.1"; havana_gene "OTTHUMG00000140314.5"; havana_transcript "OTTHUMT00000276918.4"; +chr22 HAVANA CDS 16258189 16258303 . - 1 gene_id "ENSG00000198062.10"; transcript_id "ENST00000343518.6"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "POTEH"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "POTEH-001"; exon_number 10; exon_id "ENSE00003563151.1"; level 1; protein_id "ENSP00000340610.6"; tag "basic"; tag "appris_principal"; tag "exp_conf"; tag "CCDS"; ccdsid "CCDS46658.1"; havana_gene "OTTHUMG00000140314.5"; havana_transcript "OTTHUMT00000276918.4"; +chr22 HAVANA stop_codon 16258186 16258188 . - 0 gene_id "ENSG00000198062.10"; transcript_id "ENST00000343518.6"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "POTEH"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "POTEH-001"; exon_number 10; exon_id "ENSE00003563151.1"; level 1; protein_id "ENSP00000340610.6"; tag "basic"; tag "appris_principal"; tag "exp_conf"; tag "CCDS"; ccdsid "CCDS46658.1"; havana_gene "OTTHUMG00000140314.5"; havana_transcript "OTTHUMT00000276918.4"; +chr22 HAVANA exon 16256441 16256677 . - . gene_id "ENSG00000198062.10"; transcript_id "ENST00000343518.6"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "POTEH"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "POTEH-001"; exon_number 11; exon_id "ENSE00001732273.1"; level 1; protein_id "ENSP00000340610.6"; tag "basic"; tag "appris_principal"; tag "exp_conf"; tag "CCDS"; ccdsid "CCDS46658.1"; havana_gene "OTTHUMG00000140314.5"; havana_transcript "OTTHUMT00000276918.4"; +chr22 HAVANA UTR 16287886 16287937 . - . gene_id "ENSG00000198062.10"; transcript_id "ENST00000343518.6"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "POTEH"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "POTEH-001"; level 1; protein_id "ENSP00000340610.6"; tag "basic"; tag "appris_principal"; tag "exp_conf"; tag "CCDS"; ccdsid "CCDS46658.1"; havana_gene "OTTHUMG00000140314.5"; havana_transcript "OTTHUMT00000276918.4"; +chr22 HAVANA UTR 16258185 16258188 . - . gene_id "ENSG00000198062.10"; transcript_id "ENST00000343518.6"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "POTEH"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "POTEH-001"; level 1; protein_id "ENSP00000340610.6"; tag "basic"; tag "appris_principal"; tag "exp_conf"; tag "CCDS"; ccdsid "CCDS46658.1"; havana_gene "OTTHUMG00000140314.5"; havana_transcript "OTTHUMT00000276918.4"; +chr22 HAVANA UTR 16256441 16256677 . - . gene_id "ENSG00000198062.10"; transcript_id "ENST00000343518.6"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "POTEH"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "POTEH-001"; level 1; protein_id "ENSP00000340610.6"; tag "basic"; tag "appris_principal"; tag "exp_conf"; tag "CCDS"; ccdsid "CCDS46658.1"; havana_gene "OTTHUMG00000140314.5"; havana_transcript "OTTHUMT00000276918.4"; +chr22 HAVANA gene 16274560 16278602 . + . gene_id "ENSG00000236666.1"; transcript_id "ENSG00000236666.1"; gene_type "antisense"; gene_status "NOVEL"; gene_name "POTEH-AS1"; transcript_type "antisense"; transcript_status "NOVEL"; transcript_name "POTEH-AS1"; level 2; havana_gene "OTTHUMG00000140316.1"; +chr22 HAVANA transcript 16274560 16278602 . + . gene_id "ENSG00000236666.1"; transcript_id "ENST00000422014.1"; gene_type "antisense"; gene_status "NOVEL"; gene_name "POTEH-AS1"; transcript_type "antisense"; transcript_status "KNOWN"; transcript_name "POTEH-AS1-001"; level 2; tag "basic"; havana_gene "OTTHUMG00000140316.1"; havana_transcript "OTTHUMT00000276920.1"; +chr22 HAVANA exon 16274560 16275003 . + . gene_id "ENSG00000236666.1"; transcript_id "ENST00000422014.1"; gene_type "antisense"; gene_status "NOVEL"; gene_name "POTEH-AS1"; transcript_type "antisense"; transcript_status "KNOWN"; transcript_name "POTEH-AS1-001"; exon_number 1; exon_id "ENSE00001671032.1"; level 2; tag "basic"; havana_gene "OTTHUMG00000140316.1"; havana_transcript "OTTHUMT00000276920.1"; +chr22 HAVANA exon 16276481 16278602 . + . gene_id "ENSG00000236666.1"; transcript_id "ENST00000422014.1"; gene_type "antisense"; gene_status "NOVEL"; gene_name "POTEH-AS1"; transcript_type "antisense"; transcript_status "KNOWN"; transcript_name "POTEH-AS1-001"; exon_number 2; exon_id "ENSE00001600878.1"; level 2; tag "basic"; havana_gene "OTTHUMG00000140316.1"; havana_transcript "OTTHUMT00000276920.1"; +chr22 HAVANA gene 16362385 16362561 . + . gene_id "ENSG00000226474.1"; transcript_id "ENSG00000226474.1"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "LA16c-2F2.5"; transcript_type "pseudogene"; transcript_status "KNOWN"; transcript_name "LA16c-2F2.5"; level 2; havana_gene "OTTHUMG00000140338.2"; +chr22 HAVANA transcript 16362385 16362561 . + . gene_id "ENSG00000226474.1"; transcript_id "ENST00000440999.1"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "LA16c-2F2.5"; transcript_type "unprocessed_pseudogene"; transcript_status "KNOWN"; transcript_name "LA16c-2F2.5-001"; level 2; ont "PGO:0000005"; havana_gene "OTTHUMG00000140338.2"; havana_transcript "OTTHUMT00000276962.2"; +chr22 HAVANA exon 16362385 16362561 . + . gene_id "ENSG00000226474.1"; transcript_id "ENST00000440999.1"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "LA16c-2F2.5"; transcript_type "unprocessed_pseudogene"; transcript_status "KNOWN"; transcript_name "LA16c-2F2.5-001"; exon_number 1; exon_id "ENSE00001689749.1"; level 2; ont "PGO:0000005"; havana_gene "OTTHUMG00000140338.2"; havana_transcript "OTTHUMT00000276962.2"; +chr22 HAVANA gene 16364867 16366204 . + . gene_id "ENSG00000231565.1"; transcript_id "ENSG00000231565.1"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "NEK2P2"; transcript_type "pseudogene"; transcript_status "KNOWN"; transcript_name "NEK2P2"; level 1; tag "pseudo_consens"; havana_gene "OTTHUMG00000140351.1"; +chr22 HAVANA transcript 16364867 16366204 . + . gene_id "ENSG00000231565.1"; transcript_id "ENST00000438441.1"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "NEK2P2"; transcript_type "processed_pseudogene"; transcript_status "KNOWN"; transcript_name "NEK2P2-001"; level 1; ont "PGO:0000004"; tag "pseudo_consens"; havana_gene "OTTHUMG00000140351.1"; havana_transcript "OTTHUMT00000276998.1"; +chr22 HAVANA exon 16364867 16366204 . + . gene_id "ENSG00000231565.1"; transcript_id "ENST00000438441.1"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "NEK2P2"; transcript_type "processed_pseudogene"; transcript_status "KNOWN"; transcript_name "NEK2P2-001"; exon_number 1; exon_id "ENSE00001642903.1"; level 1; ont "PGO:0000004"; tag "pseudo_consens"; havana_gene "OTTHUMG00000140351.1"; havana_transcript "OTTHUMT00000276998.1"; +chr22 HAVANA gene 16373081 16377055 . + . gene_id "ENSG00000230471.1"; transcript_id "ENSG00000230471.1"; gene_type "lincRNA"; gene_status "NOVEL"; gene_name "LA16c-2F2.8"; transcript_type "lincRNA"; transcript_status "NOVEL"; transcript_name "LA16c-2F2.8"; level 1; havana_gene "OTTHUMG00000140353.1"; +chr22 HAVANA transcript 16373081 16377055 . + . gene_id "ENSG00000230471.1"; transcript_id "ENST00000428118.1"; gene_type "lincRNA"; gene_status "NOVEL"; gene_name "LA16c-2F2.8"; transcript_type "lincRNA"; transcript_status "KNOWN"; transcript_name "LA16c-2F2.8-001"; level 1; tag "basic"; tag "exp_conf"; havana_gene "OTTHUMG00000140353.1"; havana_transcript "OTTHUMT00000277001.1"; +chr22 HAVANA exon 16373081 16373121 . + . gene_id "ENSG00000230471.1"; transcript_id "ENST00000428118.1"; gene_type "lincRNA"; gene_status "NOVEL"; gene_name "LA16c-2F2.8"; transcript_type "lincRNA"; transcript_status "KNOWN"; transcript_name "LA16c-2F2.8-001"; exon_number 1; exon_id "ENSE00001619071.1"; level 1; tag "basic"; tag "exp_conf"; havana_gene "OTTHUMG00000140353.1"; havana_transcript "OTTHUMT00000277001.1"; +chr22 HAVANA exon 16373830 16373911 . + . gene_id "ENSG00000230471.1"; transcript_id "ENST00000428118.1"; gene_type "lincRNA"; gene_status "NOVEL"; gene_name "LA16c-2F2.8"; transcript_type "lincRNA"; transcript_status "KNOWN"; transcript_name "LA16c-2F2.8-001"; exon_number 2; exon_id "ENSE00001719006.1"; level 1; tag "basic"; tag "exp_conf"; havana_gene "OTTHUMG00000140353.1"; havana_transcript "OTTHUMT00000277001.1"; +chr22 HAVANA exon 16375449 16377055 . + . gene_id "ENSG00000230471.1"; transcript_id "ENST00000428118.1"; gene_type "lincRNA"; gene_status "NOVEL"; gene_name "LA16c-2F2.8"; transcript_type "lincRNA"; transcript_status "KNOWN"; transcript_name "LA16c-2F2.8-001"; exon_number 3; exon_id "ENSE00001598108.1"; level 1; tag "basic"; tag "exp_conf"; havana_gene "OTTHUMG00000140353.1"; havana_transcript "OTTHUMT00000277001.1"; +chr22 HAVANA gene 18111621 18213388 . + . gene_id "ENSG00000099968.13"; transcript_id "ENSG00000099968.13"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BCL2L13"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BCL2L13"; level 1; havana_gene "OTTHUMG00000150088.3"; +chr22 HAVANA transcript 18111621 18178975 . + . gene_id "ENSG00000099968.13"; transcript_id "ENST00000399781.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BCL2L13"; transcript_type "processed_transcript"; transcript_status "KNOWN"; transcript_name "BCL2L13-008"; level 2; havana_gene "OTTHUMG00000150088.3"; havana_transcript "OTTHUMT00000316191.1"; +chr22 HAVANA exon 18111621 18111672 . + . gene_id "ENSG00000099968.13"; transcript_id "ENST00000399781.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BCL2L13"; transcript_type "processed_transcript"; transcript_status "KNOWN"; transcript_name "BCL2L13-008"; exon_number 1; exon_id "ENSE00001540168.1"; level 2; havana_gene "OTTHUMG00000150088.3"; havana_transcript "OTTHUMT00000316191.1"; +chr22 HAVANA exon 18120868 18121466 . + . gene_id "ENSG00000099968.13"; transcript_id "ENST00000399781.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BCL2L13"; transcript_type "processed_transcript"; transcript_status "KNOWN"; transcript_name "BCL2L13-008"; exon_number 2; exon_id "ENSE00001540171.1"; level 2; havana_gene "OTTHUMG00000150088.3"; havana_transcript "OTTHUMT00000316191.1"; +chr22 HAVANA exon 18138428 18138598 . + . gene_id "ENSG00000099968.13"; transcript_id "ENST00000399781.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BCL2L13"; transcript_type "processed_transcript"; transcript_status "KNOWN"; transcript_name "BCL2L13-008"; exon_number 3; exon_id "ENSE00003461313.1"; level 2; havana_gene "OTTHUMG00000150088.3"; havana_transcript "OTTHUMT00000316191.1"; +chr22 HAVANA exon 18165980 18166087 . + . gene_id "ENSG00000099968.13"; transcript_id "ENST00000399781.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BCL2L13"; transcript_type "processed_transcript"; transcript_status "KNOWN"; transcript_name "BCL2L13-008"; exon_number 4; exon_id "ENSE00003637389.1"; level 2; havana_gene "OTTHUMG00000150088.3"; havana_transcript "OTTHUMT00000316191.1"; +chr22 HAVANA exon 18178907 18178975 . + . gene_id "ENSG00000099968.13"; transcript_id "ENST00000399781.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BCL2L13"; transcript_type "processed_transcript"; transcript_status "KNOWN"; transcript_name "BCL2L13-008"; exon_number 5; exon_id "ENSE00001540167.1"; level 2; havana_gene "OTTHUMG00000150088.3"; havana_transcript "OTTHUMT00000316191.1"; +chr22 HAVANA transcript 18111682 18185194 . + . gene_id "ENSG00000099968.13"; transcript_id "ENST00000399782.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BCL2L13"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BCL2L13-002"; level 2; protein_id "ENSP00000382682.1"; tag "basic"; havana_gene "OTTHUMG00000150088.3"; havana_transcript "OTTHUMT00000316185.2"; +chr22 HAVANA exon 18111682 18111771 . + . gene_id "ENSG00000099968.13"; transcript_id "ENST00000399782.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BCL2L13"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BCL2L13-002"; exon_number 1; exon_id "ENSE00001540172.1"; level 2; protein_id "ENSP00000382682.1"; tag "basic"; havana_gene "OTTHUMG00000150088.3"; havana_transcript "OTTHUMT00000316185.2"; +chr22 HAVANA exon 18120868 18121466 . + . gene_id "ENSG00000099968.13"; transcript_id "ENST00000399782.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BCL2L13"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BCL2L13-002"; exon_number 2; exon_id "ENSE00001540171.1"; level 2; protein_id "ENSP00000382682.1"; tag "basic"; havana_gene "OTTHUMG00000150088.3"; havana_transcript "OTTHUMT00000316185.2"; +chr22 HAVANA exon 18138428 18138598 . + . gene_id "ENSG00000099968.13"; transcript_id "ENST00000399782.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BCL2L13"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BCL2L13-002"; exon_number 3; exon_id "ENSE00003647715.1"; level 2; protein_id "ENSP00000382682.1"; tag "basic"; havana_gene "OTTHUMG00000150088.3"; havana_transcript "OTTHUMT00000316185.2"; +chr22 HAVANA CDS 18138478 18138598 . + 0 gene_id "ENSG00000099968.13"; transcript_id "ENST00000399782.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BCL2L13"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BCL2L13-002"; exon_number 3; exon_id "ENSE00003647715.1"; level 2; protein_id "ENSP00000382682.1"; tag "basic"; havana_gene "OTTHUMG00000150088.3"; havana_transcript "OTTHUMT00000316185.2"; +chr22 HAVANA start_codon 18138478 18138480 . + 0 gene_id "ENSG00000099968.13"; transcript_id "ENST00000399782.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BCL2L13"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BCL2L13-002"; exon_number 3; exon_id "ENSE00003647715.1"; level 2; protein_id "ENSP00000382682.1"; tag "basic"; havana_gene "OTTHUMG00000150088.3"; havana_transcript "OTTHUMT00000316185.2"; +chr22 HAVANA exon 18165980 18166087 . + . gene_id "ENSG00000099968.13"; transcript_id "ENST00000399782.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BCL2L13"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BCL2L13-002"; exon_number 4; exon_id "ENSE00003693073.1"; level 2; protein_id "ENSP00000382682.1"; tag "basic"; havana_gene "OTTHUMG00000150088.3"; havana_transcript "OTTHUMT00000316185.2"; +chr22 HAVANA CDS 18165980 18166087 . + 2 gene_id "ENSG00000099968.13"; transcript_id "ENST00000399782.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BCL2L13"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BCL2L13-002"; exon_number 4; exon_id "ENSE00003693073.1"; level 2; protein_id "ENSP00000382682.1"; tag "basic"; havana_gene "OTTHUMG00000150088.3"; havana_transcript "OTTHUMT00000316185.2"; +chr22 HAVANA exon 18171752 18171908 . + . gene_id "ENSG00000099968.13"; transcript_id "ENST00000399782.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BCL2L13"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BCL2L13-002"; exon_number 5; exon_id "ENSE00003591214.1"; level 2; protein_id "ENSP00000382682.1"; tag "basic"; havana_gene "OTTHUMG00000150088.3"; havana_transcript "OTTHUMT00000316185.2"; +chr22 HAVANA CDS 18171752 18171908 . + 2 gene_id "ENSG00000099968.13"; transcript_id "ENST00000399782.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BCL2L13"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BCL2L13-002"; exon_number 5; exon_id "ENSE00003591214.1"; level 2; protein_id "ENSP00000382682.1"; tag "basic"; havana_gene "OTTHUMG00000150088.3"; havana_transcript "OTTHUMT00000316185.2"; +chr22 HAVANA exon 18178907 18178976 . + . gene_id "ENSG00000099968.13"; transcript_id "ENST00000399782.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BCL2L13"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BCL2L13-002"; exon_number 6; exon_id "ENSE00003497481.1"; level 2; protein_id "ENSP00000382682.1"; tag "basic"; havana_gene "OTTHUMG00000150088.3"; havana_transcript "OTTHUMT00000316185.2"; +chr22 HAVANA CDS 18178907 18178976 . + 1 gene_id "ENSG00000099968.13"; transcript_id "ENST00000399782.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BCL2L13"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BCL2L13-002"; exon_number 6; exon_id "ENSE00003497481.1"; level 2; protein_id "ENSP00000382682.1"; tag "basic"; havana_gene "OTTHUMG00000150088.3"; havana_transcript "OTTHUMT00000316185.2"; +chr22 HAVANA exon 18185009 18185194 . + . gene_id "ENSG00000099968.13"; transcript_id "ENST00000399782.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BCL2L13"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BCL2L13-002"; exon_number 7; exon_id "ENSE00001540169.1"; level 2; protein_id "ENSP00000382682.1"; tag "basic"; havana_gene "OTTHUMG00000150088.3"; havana_transcript "OTTHUMT00000316185.2"; +chr22 HAVANA CDS 18185009 18185155 . + 0 gene_id "ENSG00000099968.13"; transcript_id "ENST00000399782.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BCL2L13"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BCL2L13-002"; exon_number 7; exon_id "ENSE00001540169.1"; level 2; protein_id "ENSP00000382682.1"; tag "basic"; havana_gene "OTTHUMG00000150088.3"; havana_transcript "OTTHUMT00000316185.2"; +chr22 HAVANA stop_codon 18185156 18185158 . + 0 gene_id "ENSG00000099968.13"; transcript_id "ENST00000399782.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BCL2L13"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BCL2L13-002"; exon_number 7; exon_id "ENSE00001540169.1"; level 2; protein_id "ENSP00000382682.1"; tag "basic"; havana_gene "OTTHUMG00000150088.3"; havana_transcript "OTTHUMT00000316185.2"; +chr22 HAVANA UTR 18111682 18111771 . + . gene_id "ENSG00000099968.13"; transcript_id "ENST00000399782.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BCL2L13"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BCL2L13-002"; level 2; protein_id "ENSP00000382682.1"; tag "basic"; havana_gene "OTTHUMG00000150088.3"; havana_transcript "OTTHUMT00000316185.2"; +chr22 HAVANA UTR 18120868 18121466 . + . gene_id "ENSG00000099968.13"; transcript_id "ENST00000399782.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BCL2L13"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BCL2L13-002"; level 2; protein_id "ENSP00000382682.1"; tag "basic"; havana_gene "OTTHUMG00000150088.3"; havana_transcript "OTTHUMT00000316185.2"; +chr22 HAVANA UTR 18138428 18138477 . + . gene_id "ENSG00000099968.13"; transcript_id "ENST00000399782.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BCL2L13"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BCL2L13-002"; level 2; protein_id "ENSP00000382682.1"; tag "basic"; havana_gene "OTTHUMG00000150088.3"; havana_transcript "OTTHUMT00000316185.2"; +chr22 HAVANA UTR 18185156 18185194 . + . gene_id "ENSG00000099968.13"; transcript_id "ENST00000399782.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BCL2L13"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BCL2L13-002"; level 2; protein_id "ENSP00000382682.1"; tag "basic"; havana_gene "OTTHUMG00000150088.3"; havana_transcript "OTTHUMT00000316185.2"; +chr22 HAVANA transcript 18121356 18211487 . + . gene_id "ENSG00000099968.13"; transcript_id "ENST00000317582.5"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BCL2L13"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BCL2L13-001"; level 2; protein_id "ENSP00000318883.5"; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS13746.1"; havana_gene "OTTHUMG00000150088.3"; havana_transcript "OTTHUMT00000316184.1"; +chr22 HAVANA exon 18121356 18121652 . + . gene_id "ENSG00000099968.13"; transcript_id "ENST00000317582.5"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BCL2L13"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BCL2L13-001"; exon_number 1; exon_id "ENSE00001898002.1"; level 2; protein_id "ENSP00000318883.5"; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS13746.1"; havana_gene "OTTHUMG00000150088.3"; havana_transcript "OTTHUMT00000316184.1"; +chr22 HAVANA exon 18138428 18138598 . + . gene_id "ENSG00000099968.13"; transcript_id "ENST00000317582.5"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BCL2L13"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BCL2L13-001"; exon_number 2; exon_id "ENSE00003647715.1"; level 2; protein_id "ENSP00000318883.5"; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS13746.1"; havana_gene "OTTHUMG00000150088.3"; havana_transcript "OTTHUMT00000316184.1"; +chr22 HAVANA CDS 18138478 18138598 . + 0 gene_id "ENSG00000099968.13"; transcript_id "ENST00000317582.5"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BCL2L13"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BCL2L13-001"; exon_number 2; exon_id "ENSE00003647715.1"; level 2; protein_id "ENSP00000318883.5"; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS13746.1"; havana_gene "OTTHUMG00000150088.3"; havana_transcript "OTTHUMT00000316184.1"; +chr22 HAVANA start_codon 18138478 18138480 . + 0 gene_id "ENSG00000099968.13"; transcript_id "ENST00000317582.5"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BCL2L13"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BCL2L13-001"; exon_number 2; exon_id "ENSE00003647715.1"; level 2; protein_id "ENSP00000318883.5"; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS13746.1"; havana_gene "OTTHUMG00000150088.3"; havana_transcript "OTTHUMT00000316184.1"; +chr22 HAVANA exon 18165980 18166087 . + . gene_id "ENSG00000099968.13"; transcript_id "ENST00000317582.5"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BCL2L13"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BCL2L13-001"; exon_number 3; exon_id "ENSE00003693073.1"; level 2; protein_id "ENSP00000318883.5"; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS13746.1"; havana_gene "OTTHUMG00000150088.3"; havana_transcript "OTTHUMT00000316184.1"; +chr22 HAVANA CDS 18165980 18166087 . + 2 gene_id "ENSG00000099968.13"; transcript_id "ENST00000317582.5"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BCL2L13"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BCL2L13-001"; exon_number 3; exon_id "ENSE00003693073.1"; level 2; protein_id "ENSP00000318883.5"; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS13746.1"; havana_gene "OTTHUMG00000150088.3"; havana_transcript "OTTHUMT00000316184.1"; +chr22 HAVANA exon 18171752 18171908 . + . gene_id "ENSG00000099968.13"; transcript_id "ENST00000317582.5"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BCL2L13"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BCL2L13-001"; exon_number 4; exon_id "ENSE00003591214.1"; level 2; protein_id "ENSP00000318883.5"; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS13746.1"; havana_gene "OTTHUMG00000150088.3"; havana_transcript "OTTHUMT00000316184.1"; +chr22 HAVANA CDS 18171752 18171908 . + 2 gene_id "ENSG00000099968.13"; transcript_id "ENST00000317582.5"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BCL2L13"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BCL2L13-001"; exon_number 4; exon_id "ENSE00003591214.1"; level 2; protein_id "ENSP00000318883.5"; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS13746.1"; havana_gene "OTTHUMG00000150088.3"; havana_transcript "OTTHUMT00000316184.1"; +chr22 HAVANA exon 18178907 18178976 . + . gene_id "ENSG00000099968.13"; transcript_id "ENST00000317582.5"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BCL2L13"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BCL2L13-001"; exon_number 5; exon_id "ENSE00003497481.1"; level 2; protein_id "ENSP00000318883.5"; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS13746.1"; havana_gene "OTTHUMG00000150088.3"; havana_transcript "OTTHUMT00000316184.1"; +chr22 HAVANA CDS 18178907 18178976 . + 1 gene_id "ENSG00000099968.13"; transcript_id "ENST00000317582.5"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BCL2L13"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BCL2L13-001"; exon_number 5; exon_id "ENSE00003497481.1"; level 2; protein_id "ENSP00000318883.5"; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS13746.1"; havana_gene "OTTHUMG00000150088.3"; havana_transcript "OTTHUMT00000316184.1"; +chr22 HAVANA exon 18185009 18185152 . + . gene_id "ENSG00000099968.13"; transcript_id "ENST00000317582.5"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BCL2L13"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BCL2L13-001"; exon_number 6; exon_id "ENSE00003546934.1"; level 2; protein_id "ENSP00000318883.5"; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS13746.1"; havana_gene "OTTHUMG00000150088.3"; havana_transcript "OTTHUMT00000316184.1"; +chr22 HAVANA CDS 18185009 18185152 . + 0 gene_id "ENSG00000099968.13"; transcript_id "ENST00000317582.5"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BCL2L13"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BCL2L13-001"; exon_number 6; exon_id "ENSE00003546934.1"; level 2; protein_id "ENSP00000318883.5"; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS13746.1"; havana_gene "OTTHUMG00000150088.3"; havana_transcript "OTTHUMT00000316184.1"; +chr22 HAVANA exon 18209443 18211487 . + . gene_id "ENSG00000099968.13"; transcript_id "ENST00000317582.5"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BCL2L13"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BCL2L13-001"; exon_number 7; exon_id "ENSE00001680488.2"; level 2; protein_id "ENSP00000318883.5"; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS13746.1"; havana_gene "OTTHUMG00000150088.3"; havana_transcript "OTTHUMT00000316184.1"; +chr22 HAVANA CDS 18209443 18210297 . + 0 gene_id "ENSG00000099968.13"; transcript_id "ENST00000317582.5"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BCL2L13"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BCL2L13-001"; exon_number 7; exon_id "ENSE00001680488.2"; level 2; protein_id "ENSP00000318883.5"; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS13746.1"; havana_gene "OTTHUMG00000150088.3"; havana_transcript "OTTHUMT00000316184.1"; +chr22 HAVANA stop_codon 18210298 18210300 . + 0 gene_id "ENSG00000099968.13"; transcript_id "ENST00000317582.5"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BCL2L13"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BCL2L13-001"; exon_number 7; exon_id "ENSE00001680488.2"; level 2; protein_id "ENSP00000318883.5"; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS13746.1"; havana_gene "OTTHUMG00000150088.3"; havana_transcript "OTTHUMT00000316184.1"; +chr22 HAVANA UTR 18121356 18121652 . + . gene_id "ENSG00000099968.13"; transcript_id "ENST00000317582.5"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BCL2L13"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BCL2L13-001"; level 2; protein_id "ENSP00000318883.5"; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS13746.1"; havana_gene "OTTHUMG00000150088.3"; havana_transcript "OTTHUMT00000316184.1"; +chr22 HAVANA UTR 18138428 18138477 . + . gene_id "ENSG00000099968.13"; transcript_id "ENST00000317582.5"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BCL2L13"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BCL2L13-001"; level 2; protein_id "ENSP00000318883.5"; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS13746.1"; havana_gene "OTTHUMG00000150088.3"; havana_transcript "OTTHUMT00000316184.1"; +chr22 HAVANA UTR 18210298 18211487 . + . gene_id "ENSG00000099968.13"; transcript_id "ENST00000317582.5"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BCL2L13"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BCL2L13-001"; level 2; protein_id "ENSP00000318883.5"; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS13746.1"; havana_gene "OTTHUMG00000150088.3"; havana_transcript "OTTHUMT00000316184.1"; +chr22 HAVANA transcript 18121507 18211465 . + . gene_id "ENSG00000099968.13"; transcript_id "ENST00000498133.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BCL2L13"; transcript_type "nonsense_mediated_decay"; transcript_status "KNOWN"; transcript_name "BCL2L13-003"; level 2; protein_id "ENSP00000436321.1"; havana_gene "OTTHUMG00000150088.3"; havana_transcript "OTTHUMT00000316186.2"; +chr22 HAVANA exon 18121507 18121652 . + . gene_id "ENSG00000099968.13"; transcript_id "ENST00000498133.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BCL2L13"; transcript_type "nonsense_mediated_decay"; transcript_status "KNOWN"; transcript_name "BCL2L13-003"; exon_number 1; exon_id "ENSE00001412972.2"; level 2; protein_id "ENSP00000436321.1"; havana_gene "OTTHUMG00000150088.3"; havana_transcript "OTTHUMT00000316186.2"; +chr22 HAVANA exon 18138428 18138598 . + . gene_id "ENSG00000099968.13"; transcript_id "ENST00000498133.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BCL2L13"; transcript_type "nonsense_mediated_decay"; transcript_status "KNOWN"; transcript_name "BCL2L13-003"; exon_number 2; exon_id "ENSE00003647715.1"; level 2; protein_id "ENSP00000436321.1"; havana_gene "OTTHUMG00000150088.3"; havana_transcript "OTTHUMT00000316186.2"; +chr22 HAVANA CDS 18138478 18138598 . + 0 gene_id "ENSG00000099968.13"; transcript_id "ENST00000498133.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BCL2L13"; transcript_type "nonsense_mediated_decay"; transcript_status "KNOWN"; transcript_name "BCL2L13-003"; exon_number 2; exon_id "ENSE00003647715.1"; level 2; protein_id "ENSP00000436321.1"; havana_gene "OTTHUMG00000150088.3"; havana_transcript "OTTHUMT00000316186.2"; +chr22 HAVANA start_codon 18138478 18138480 . + 0 gene_id "ENSG00000099968.13"; transcript_id "ENST00000498133.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BCL2L13"; transcript_type "nonsense_mediated_decay"; transcript_status "KNOWN"; transcript_name "BCL2L13-003"; exon_number 2; exon_id "ENSE00003647715.1"; level 2; protein_id "ENSP00000436321.1"; havana_gene "OTTHUMG00000150088.3"; havana_transcript "OTTHUMT00000316186.2"; +chr22 HAVANA exon 18165980 18166087 . + . gene_id "ENSG00000099968.13"; transcript_id "ENST00000498133.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BCL2L13"; transcript_type "nonsense_mediated_decay"; transcript_status "KNOWN"; transcript_name "BCL2L13-003"; exon_number 3; exon_id "ENSE00003693073.1"; level 2; protein_id "ENSP00000436321.1"; havana_gene "OTTHUMG00000150088.3"; havana_transcript "OTTHUMT00000316186.2"; +chr22 HAVANA CDS 18165980 18166087 . + 2 gene_id "ENSG00000099968.13"; transcript_id "ENST00000498133.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BCL2L13"; transcript_type "nonsense_mediated_decay"; transcript_status "KNOWN"; transcript_name "BCL2L13-003"; exon_number 3; exon_id "ENSE00003693073.1"; level 2; protein_id "ENSP00000436321.1"; havana_gene "OTTHUMG00000150088.3"; havana_transcript "OTTHUMT00000316186.2"; +chr22 HAVANA exon 18178907 18178976 . + . gene_id "ENSG00000099968.13"; transcript_id "ENST00000498133.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BCL2L13"; transcript_type "nonsense_mediated_decay"; transcript_status "KNOWN"; transcript_name "BCL2L13-003"; exon_number 4; exon_id "ENSE00003460053.1"; level 2; protein_id "ENSP00000436321.1"; havana_gene "OTTHUMG00000150088.3"; havana_transcript "OTTHUMT00000316186.2"; +chr22 HAVANA CDS 18178907 18178911 . + 2 gene_id "ENSG00000099968.13"; transcript_id "ENST00000498133.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BCL2L13"; transcript_type "nonsense_mediated_decay"; transcript_status "KNOWN"; transcript_name "BCL2L13-003"; exon_number 4; exon_id "ENSE00003460053.1"; level 2; protein_id "ENSP00000436321.1"; havana_gene "OTTHUMG00000150088.3"; havana_transcript "OTTHUMT00000316186.2"; +chr22 HAVANA stop_codon 18178912 18178914 . + 0 gene_id "ENSG00000099968.13"; transcript_id "ENST00000498133.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BCL2L13"; transcript_type "nonsense_mediated_decay"; transcript_status "KNOWN"; transcript_name "BCL2L13-003"; exon_number 4; exon_id "ENSE00003460053.1"; level 2; protein_id "ENSP00000436321.1"; havana_gene "OTTHUMG00000150088.3"; havana_transcript "OTTHUMT00000316186.2"; +chr22 HAVANA exon 18185009 18185152 . + . gene_id "ENSG00000099968.13"; transcript_id "ENST00000498133.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BCL2L13"; transcript_type "nonsense_mediated_decay"; transcript_status "KNOWN"; transcript_name "BCL2L13-003"; exon_number 5; exon_id "ENSE00003503185.1"; level 2; protein_id "ENSP00000436321.1"; havana_gene "OTTHUMG00000150088.3"; havana_transcript "OTTHUMT00000316186.2"; +chr22 HAVANA exon 18209443 18211465 . + . gene_id "ENSG00000099968.13"; transcript_id "ENST00000498133.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BCL2L13"; transcript_type "nonsense_mediated_decay"; transcript_status "KNOWN"; transcript_name "BCL2L13-003"; exon_number 6; exon_id "ENSE00003520084.1"; level 2; protein_id "ENSP00000436321.1"; havana_gene "OTTHUMG00000150088.3"; havana_transcript "OTTHUMT00000316186.2"; +chr22 HAVANA UTR 18121507 18121652 . + . gene_id "ENSG00000099968.13"; transcript_id "ENST00000498133.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BCL2L13"; transcript_type "nonsense_mediated_decay"; transcript_status "KNOWN"; transcript_name "BCL2L13-003"; level 2; protein_id "ENSP00000436321.1"; havana_gene "OTTHUMG00000150088.3"; havana_transcript "OTTHUMT00000316186.2"; +chr22 HAVANA UTR 18138428 18138477 . + . gene_id "ENSG00000099968.13"; transcript_id "ENST00000498133.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BCL2L13"; transcript_type "nonsense_mediated_decay"; transcript_status "KNOWN"; transcript_name "BCL2L13-003"; level 2; protein_id "ENSP00000436321.1"; havana_gene "OTTHUMG00000150088.3"; havana_transcript "OTTHUMT00000316186.2"; +chr22 HAVANA UTR 18178912 18178976 . + . gene_id "ENSG00000099968.13"; transcript_id "ENST00000498133.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BCL2L13"; transcript_type "nonsense_mediated_decay"; transcript_status "KNOWN"; transcript_name "BCL2L13-003"; level 2; protein_id "ENSP00000436321.1"; havana_gene "OTTHUMG00000150088.3"; havana_transcript "OTTHUMT00000316186.2"; +chr22 HAVANA UTR 18185009 18185152 . + . gene_id "ENSG00000099968.13"; transcript_id "ENST00000498133.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BCL2L13"; transcript_type "nonsense_mediated_decay"; transcript_status "KNOWN"; transcript_name "BCL2L13-003"; level 2; protein_id "ENSP00000436321.1"; havana_gene "OTTHUMG00000150088.3"; havana_transcript "OTTHUMT00000316186.2"; +chr22 HAVANA UTR 18209443 18211465 . + . gene_id "ENSG00000099968.13"; transcript_id "ENST00000498133.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BCL2L13"; transcript_type "nonsense_mediated_decay"; transcript_status "KNOWN"; transcript_name "BCL2L13-003"; level 2; protein_id "ENSP00000436321.1"; havana_gene "OTTHUMG00000150088.3"; havana_transcript "OTTHUMT00000316186.2"; +chr22 ENSEMBL transcript 18121507 18211465 . + . gene_id "ENSG00000099968.13"; transcript_id "ENST00000543133.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BCL2L13"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BCL2L13-204"; level 3; protein_id "ENSP00000437667.1"; tag "basic"; tag "CCDS"; ccdsid "CCDS59448.1"; havana_gene "OTTHUMG00000150088.3"; +chr22 ENSEMBL exon 18121507 18121652 . + . gene_id "ENSG00000099968.13"; transcript_id "ENST00000543133.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BCL2L13"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BCL2L13-204"; exon_number 1; exon_id "ENSE00001412972.2"; level 3; protein_id "ENSP00000437667.1"; tag "basic"; tag "CCDS"; ccdsid "CCDS59448.1"; havana_gene "OTTHUMG00000150088.3"; +chr22 ENSEMBL exon 18138428 18138598 . + . gene_id "ENSG00000099968.13"; transcript_id "ENST00000543133.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BCL2L13"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BCL2L13-204"; exon_number 2; exon_id "ENSE00003461313.1"; level 3; protein_id "ENSP00000437667.1"; tag "basic"; tag "CCDS"; ccdsid "CCDS59448.1"; havana_gene "OTTHUMG00000150088.3"; +chr22 ENSEMBL exon 18165980 18166087 . + . gene_id "ENSG00000099968.13"; transcript_id "ENST00000543133.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BCL2L13"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BCL2L13-204"; exon_number 3; exon_id "ENSE00003637389.1"; level 3; protein_id "ENSP00000437667.1"; tag "basic"; tag "CCDS"; ccdsid "CCDS59448.1"; havana_gene "OTTHUMG00000150088.3"; +chr22 ENSEMBL exon 18178907 18178976 . + . gene_id "ENSG00000099968.13"; transcript_id "ENST00000543133.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BCL2L13"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BCL2L13-204"; exon_number 4; exon_id "ENSE00003555903.1"; level 3; protein_id "ENSP00000437667.1"; tag "basic"; tag "CCDS"; ccdsid "CCDS59448.1"; havana_gene "OTTHUMG00000150088.3"; +chr22 ENSEMBL exon 18185009 18185152 . + . gene_id "ENSG00000099968.13"; transcript_id "ENST00000543133.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BCL2L13"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BCL2L13-204"; exon_number 5; exon_id "ENSE00003600296.1"; level 3; protein_id "ENSP00000437667.1"; tag "basic"; tag "CCDS"; ccdsid "CCDS59448.1"; havana_gene "OTTHUMG00000150088.3"; +chr22 ENSEMBL CDS 18185039 18185152 . + 0 gene_id "ENSG00000099968.13"; transcript_id "ENST00000543133.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BCL2L13"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BCL2L13-204"; exon_number 5; exon_id "ENSE00003600296.1"; level 3; protein_id "ENSP00000437667.1"; tag "basic"; tag "CCDS"; ccdsid "CCDS59448.1"; havana_gene "OTTHUMG00000150088.3"; +chr22 ENSEMBL start_codon 18185039 18185041 . + 0 gene_id "ENSG00000099968.13"; transcript_id "ENST00000543133.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BCL2L13"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BCL2L13-204"; exon_number 5; exon_id "ENSE00003600296.1"; level 3; protein_id "ENSP00000437667.1"; tag "basic"; tag "CCDS"; ccdsid "CCDS59448.1"; havana_gene "OTTHUMG00000150088.3"; +chr22 ENSEMBL exon 18209443 18211465 . + . gene_id "ENSG00000099968.13"; transcript_id "ENST00000543133.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BCL2L13"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BCL2L13-204"; exon_number 6; exon_id "ENSE00003626534.1"; level 3; protein_id "ENSP00000437667.1"; tag "basic"; tag "CCDS"; ccdsid "CCDS59448.1"; havana_gene "OTTHUMG00000150088.3"; +chr22 ENSEMBL CDS 18209443 18210297 . + 0 gene_id "ENSG00000099968.13"; transcript_id "ENST00000543133.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BCL2L13"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BCL2L13-204"; exon_number 6; exon_id "ENSE00003626534.1"; level 3; protein_id "ENSP00000437667.1"; tag "basic"; tag "CCDS"; ccdsid "CCDS59448.1"; havana_gene "OTTHUMG00000150088.3"; +chr22 ENSEMBL stop_codon 18210298 18210300 . + 0 gene_id "ENSG00000099968.13"; transcript_id "ENST00000543133.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BCL2L13"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BCL2L13-204"; exon_number 6; exon_id "ENSE00003626534.1"; level 3; protein_id "ENSP00000437667.1"; tag "basic"; tag "CCDS"; ccdsid "CCDS59448.1"; havana_gene "OTTHUMG00000150088.3"; +chr22 ENSEMBL UTR 18121507 18121652 . + . gene_id "ENSG00000099968.13"; transcript_id "ENST00000543133.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BCL2L13"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BCL2L13-204"; level 3; protein_id "ENSP00000437667.1"; tag "basic"; tag "CCDS"; ccdsid "CCDS59448.1"; havana_gene "OTTHUMG00000150088.3"; +chr22 ENSEMBL UTR 18138428 18138598 . + . gene_id "ENSG00000099968.13"; transcript_id "ENST00000543133.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BCL2L13"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BCL2L13-204"; level 3; protein_id "ENSP00000437667.1"; tag "basic"; tag "CCDS"; ccdsid "CCDS59448.1"; havana_gene "OTTHUMG00000150088.3"; +chr22 ENSEMBL UTR 18165980 18166087 . + . gene_id "ENSG00000099968.13"; transcript_id "ENST00000543133.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BCL2L13"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BCL2L13-204"; level 3; protein_id "ENSP00000437667.1"; tag "basic"; tag "CCDS"; ccdsid "CCDS59448.1"; havana_gene "OTTHUMG00000150088.3"; +chr22 ENSEMBL UTR 18178907 18178976 . + . gene_id "ENSG00000099968.13"; transcript_id "ENST00000543133.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BCL2L13"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BCL2L13-204"; level 3; protein_id "ENSP00000437667.1"; tag "basic"; tag "CCDS"; ccdsid "CCDS59448.1"; havana_gene "OTTHUMG00000150088.3"; +chr22 ENSEMBL UTR 18185009 18185038 . + . gene_id "ENSG00000099968.13"; transcript_id "ENST00000543133.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BCL2L13"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BCL2L13-204"; level 3; protein_id "ENSP00000437667.1"; tag "basic"; tag "CCDS"; ccdsid "CCDS59448.1"; havana_gene "OTTHUMG00000150088.3"; +chr22 ENSEMBL UTR 18210298 18211465 . + . gene_id "ENSG00000099968.13"; transcript_id "ENST00000543133.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BCL2L13"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BCL2L13-204"; level 3; protein_id "ENSP00000437667.1"; tag "basic"; tag "CCDS"; ccdsid "CCDS59448.1"; havana_gene "OTTHUMG00000150088.3"; +chr22 HAVANA transcript 18121523 18175161 . + . gene_id "ENSG00000099968.13"; transcript_id "ENST00000464649.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BCL2L13"; transcript_type "processed_transcript"; transcript_status "PUTATIVE"; transcript_name "BCL2L13-009"; level 2; havana_gene "OTTHUMG00000150088.3"; havana_transcript "OTTHUMT00000316192.1"; +chr22 HAVANA exon 18121523 18121652 . + . gene_id "ENSG00000099968.13"; transcript_id "ENST00000464649.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BCL2L13"; transcript_type "processed_transcript"; transcript_status "PUTATIVE"; transcript_name "BCL2L13-009"; exon_number 1; exon_id "ENSE00001845131.1"; level 2; havana_gene "OTTHUMG00000150088.3"; havana_transcript "OTTHUMT00000316192.1"; +chr22 HAVANA exon 18165980 18166087 . + . gene_id "ENSG00000099968.13"; transcript_id "ENST00000464649.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BCL2L13"; transcript_type "processed_transcript"; transcript_status "PUTATIVE"; transcript_name "BCL2L13-009"; exon_number 2; exon_id "ENSE00003637389.1"; level 2; havana_gene "OTTHUMG00000150088.3"; havana_transcript "OTTHUMT00000316192.1"; +chr22 HAVANA exon 18171752 18171908 . + . gene_id "ENSG00000099968.13"; transcript_id "ENST00000464649.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BCL2L13"; transcript_type "processed_transcript"; transcript_status "PUTATIVE"; transcript_name "BCL2L13-009"; exon_number 3; exon_id "ENSE00003687973.1"; level 2; havana_gene "OTTHUMG00000150088.3"; havana_transcript "OTTHUMT00000316192.1"; +chr22 HAVANA exon 18175122 18175161 . + . gene_id "ENSG00000099968.13"; transcript_id "ENST00000464649.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BCL2L13"; transcript_type "processed_transcript"; transcript_status "PUTATIVE"; transcript_name "BCL2L13-009"; exon_number 4; exon_id "ENSE00001873289.1"; level 2; havana_gene "OTTHUMG00000150088.3"; havana_transcript "OTTHUMT00000316192.1"; +chr22 ENSEMBL transcript 18121523 18210466 . + . gene_id "ENSG00000099968.13"; transcript_id "ENST00000538149.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BCL2L13"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BCL2L13-203"; level 3; protein_id "ENSP00000441344.1"; tag "basic"; havana_gene "OTTHUMG00000150088.3"; +chr22 ENSEMBL exon 18121523 18121652 . + . gene_id "ENSG00000099968.13"; transcript_id "ENST00000538149.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BCL2L13"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BCL2L13-203"; exon_number 1; exon_id "ENSE00001845131.1"; level 3; protein_id "ENSP00000441344.1"; tag "basic"; havana_gene "OTTHUMG00000150088.3"; +chr22 ENSEMBL exon 18138428 18138598 . + . gene_id "ENSG00000099968.13"; transcript_id "ENST00000538149.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BCL2L13"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BCL2L13-203"; exon_number 2; exon_id "ENSE00003461014.1"; level 3; protein_id "ENSP00000441344.1"; tag "basic"; havana_gene "OTTHUMG00000150088.3"; +chr22 ENSEMBL CDS 18138515 18138598 . + 0 gene_id "ENSG00000099968.13"; transcript_id "ENST00000538149.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BCL2L13"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BCL2L13-203"; exon_number 2; exon_id "ENSE00003461014.1"; level 3; protein_id "ENSP00000441344.1"; tag "basic"; havana_gene "OTTHUMG00000150088.3"; +chr22 ENSEMBL start_codon 18138515 18138517 . + 0 gene_id "ENSG00000099968.13"; transcript_id "ENST00000538149.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BCL2L13"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BCL2L13-203"; exon_number 2; exon_id "ENSE00003461014.1"; level 3; protein_id "ENSP00000441344.1"; tag "basic"; havana_gene "OTTHUMG00000150088.3"; +chr22 ENSEMBL exon 18185009 18185152 . + . gene_id "ENSG00000099968.13"; transcript_id "ENST00000538149.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BCL2L13"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BCL2L13-203"; exon_number 3; exon_id "ENSE00003546934.1"; level 3; protein_id "ENSP00000441344.1"; tag "basic"; havana_gene "OTTHUMG00000150088.3"; +chr22 ENSEMBL CDS 18185009 18185152 . + 0 gene_id "ENSG00000099968.13"; transcript_id "ENST00000538149.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BCL2L13"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BCL2L13-203"; exon_number 3; exon_id "ENSE00003546934.1"; level 3; protein_id "ENSP00000441344.1"; tag "basic"; havana_gene "OTTHUMG00000150088.3"; +chr22 ENSEMBL exon 18209443 18210466 . + . gene_id "ENSG00000099968.13"; transcript_id "ENST00000538149.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BCL2L13"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BCL2L13-203"; exon_number 4; exon_id "ENSE00002232124.1"; level 3; protein_id "ENSP00000441344.1"; tag "basic"; havana_gene "OTTHUMG00000150088.3"; +chr22 ENSEMBL CDS 18209443 18210297 . + 0 gene_id "ENSG00000099968.13"; transcript_id "ENST00000538149.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BCL2L13"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BCL2L13-203"; exon_number 4; exon_id "ENSE00002232124.1"; level 3; protein_id "ENSP00000441344.1"; tag "basic"; havana_gene "OTTHUMG00000150088.3"; +chr22 ENSEMBL stop_codon 18210298 18210300 . + 0 gene_id "ENSG00000099968.13"; transcript_id "ENST00000538149.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BCL2L13"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BCL2L13-203"; exon_number 4; exon_id "ENSE00002232124.1"; level 3; protein_id "ENSP00000441344.1"; tag "basic"; havana_gene "OTTHUMG00000150088.3"; +chr22 ENSEMBL UTR 18121523 18121652 . + . gene_id "ENSG00000099968.13"; transcript_id "ENST00000538149.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BCL2L13"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BCL2L13-203"; level 3; protein_id "ENSP00000441344.1"; tag "basic"; havana_gene "OTTHUMG00000150088.3"; +chr22 ENSEMBL UTR 18138428 18138514 . + . gene_id "ENSG00000099968.13"; transcript_id "ENST00000538149.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BCL2L13"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BCL2L13-203"; level 3; protein_id "ENSP00000441344.1"; tag "basic"; havana_gene "OTTHUMG00000150088.3"; +chr22 ENSEMBL UTR 18210298 18210466 . + . gene_id "ENSG00000099968.13"; transcript_id "ENST00000538149.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BCL2L13"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BCL2L13-203"; level 3; protein_id "ENSP00000441344.1"; tag "basic"; havana_gene "OTTHUMG00000150088.3"; +chr22 ENSEMBL transcript 18121530 18210428 . + . gene_id "ENSG00000099968.13"; transcript_id "ENST00000337612.5"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BCL2L13"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BCL2L13-201"; level 3; protein_id "ENSP00000338932.5"; tag "basic"; tag "CCDS"; ccdsid "CCDS59448.1"; havana_gene "OTTHUMG00000150088.3"; +chr22 ENSEMBL exon 18121530 18121652 . + . gene_id "ENSG00000099968.13"; transcript_id "ENST00000337612.5"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BCL2L13"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BCL2L13-201"; exon_number 1; exon_id "ENSE00001323953.3"; level 3; protein_id "ENSP00000338932.5"; tag "basic"; tag "CCDS"; ccdsid "CCDS59448.1"; havana_gene "OTTHUMG00000150088.3"; +chr22 ENSEMBL exon 18138428 18138598 . + . gene_id "ENSG00000099968.13"; transcript_id "ENST00000337612.5"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BCL2L13"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BCL2L13-201"; exon_number 2; exon_id "ENSE00003461313.1"; level 3; protein_id "ENSP00000338932.5"; tag "basic"; tag "CCDS"; ccdsid "CCDS59448.1"; havana_gene "OTTHUMG00000150088.3"; +chr22 ENSEMBL exon 18165980 18166087 . + . gene_id "ENSG00000099968.13"; transcript_id "ENST00000337612.5"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BCL2L13"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BCL2L13-201"; exon_number 3; exon_id "ENSE00003637389.1"; level 3; protein_id "ENSP00000338932.5"; tag "basic"; tag "CCDS"; ccdsid "CCDS59448.1"; havana_gene "OTTHUMG00000150088.3"; +chr22 ENSEMBL exon 18185009 18185152 . + . gene_id "ENSG00000099968.13"; transcript_id "ENST00000337612.5"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BCL2L13"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BCL2L13-201"; exon_number 4; exon_id "ENSE00003600296.1"; level 3; protein_id "ENSP00000338932.5"; tag "basic"; tag "CCDS"; ccdsid "CCDS59448.1"; havana_gene "OTTHUMG00000150088.3"; +chr22 ENSEMBL CDS 18185039 18185152 . + 0 gene_id "ENSG00000099968.13"; transcript_id "ENST00000337612.5"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BCL2L13"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BCL2L13-201"; exon_number 4; exon_id "ENSE00003600296.1"; level 3; protein_id "ENSP00000338932.5"; tag "basic"; tag "CCDS"; ccdsid "CCDS59448.1"; havana_gene "OTTHUMG00000150088.3"; +chr22 ENSEMBL start_codon 18185039 18185041 . + 0 gene_id "ENSG00000099968.13"; transcript_id "ENST00000337612.5"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BCL2L13"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BCL2L13-201"; exon_number 4; exon_id "ENSE00003600296.1"; level 3; protein_id "ENSP00000338932.5"; tag "basic"; tag "CCDS"; ccdsid "CCDS59448.1"; havana_gene "OTTHUMG00000150088.3"; +chr22 ENSEMBL exon 18209443 18210428 . + . gene_id "ENSG00000099968.13"; transcript_id "ENST00000337612.5"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BCL2L13"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BCL2L13-201"; exon_number 5; exon_id "ENSE00002263893.1"; level 3; protein_id "ENSP00000338932.5"; tag "basic"; tag "CCDS"; ccdsid "CCDS59448.1"; havana_gene "OTTHUMG00000150088.3"; +chr22 ENSEMBL CDS 18209443 18210297 . + 0 gene_id "ENSG00000099968.13"; transcript_id "ENST00000337612.5"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BCL2L13"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BCL2L13-201"; exon_number 5; exon_id "ENSE00002263893.1"; level 3; protein_id "ENSP00000338932.5"; tag "basic"; tag "CCDS"; ccdsid "CCDS59448.1"; havana_gene "OTTHUMG00000150088.3"; +chr22 ENSEMBL stop_codon 18210298 18210300 . + 0 gene_id "ENSG00000099968.13"; transcript_id "ENST00000337612.5"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BCL2L13"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BCL2L13-201"; exon_number 5; exon_id "ENSE00002263893.1"; level 3; protein_id "ENSP00000338932.5"; tag "basic"; tag "CCDS"; ccdsid "CCDS59448.1"; havana_gene "OTTHUMG00000150088.3"; +chr22 ENSEMBL UTR 18121530 18121652 . + . gene_id "ENSG00000099968.13"; transcript_id "ENST00000337612.5"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BCL2L13"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BCL2L13-201"; level 3; protein_id "ENSP00000338932.5"; tag "basic"; tag "CCDS"; ccdsid "CCDS59448.1"; havana_gene "OTTHUMG00000150088.3"; +chr22 ENSEMBL UTR 18138428 18138598 . + . gene_id "ENSG00000099968.13"; transcript_id "ENST00000337612.5"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BCL2L13"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BCL2L13-201"; level 3; protein_id "ENSP00000338932.5"; tag "basic"; tag "CCDS"; ccdsid "CCDS59448.1"; havana_gene "OTTHUMG00000150088.3"; +chr22 ENSEMBL UTR 18165980 18166087 . + . gene_id "ENSG00000099968.13"; transcript_id "ENST00000337612.5"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BCL2L13"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BCL2L13-201"; level 3; protein_id "ENSP00000338932.5"; tag "basic"; tag "CCDS"; ccdsid "CCDS59448.1"; havana_gene "OTTHUMG00000150088.3"; +chr22 ENSEMBL UTR 18185009 18185038 . + . gene_id "ENSG00000099968.13"; transcript_id "ENST00000337612.5"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BCL2L13"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BCL2L13-201"; level 3; protein_id "ENSP00000338932.5"; tag "basic"; tag "CCDS"; ccdsid "CCDS59448.1"; havana_gene "OTTHUMG00000150088.3"; +chr22 ENSEMBL UTR 18210298 18210428 . + . gene_id "ENSG00000099968.13"; transcript_id "ENST00000337612.5"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BCL2L13"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BCL2L13-201"; level 3; protein_id "ENSP00000338932.5"; tag "basic"; tag "CCDS"; ccdsid "CCDS59448.1"; havana_gene "OTTHUMG00000150088.3"; +chr22 HAVANA transcript 18121538 18186499 . + . gene_id "ENSG00000099968.13"; transcript_id "ENST00000493680.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BCL2L13"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BCL2L13-004"; level 2; protein_id "ENSP00000434764.1"; tag "alternative_5_UTR"; tag "basic"; havana_gene "OTTHUMG00000150088.3"; havana_transcript "OTTHUMT00000316187.2"; +chr22 HAVANA exon 18121538 18121652 . + . gene_id "ENSG00000099968.13"; transcript_id "ENST00000493680.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BCL2L13"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BCL2L13-004"; exon_number 1; exon_id "ENSE00001854798.1"; level 2; protein_id "ENSP00000434764.1"; tag "alternative_5_UTR"; tag "basic"; havana_gene "OTTHUMG00000150088.3"; havana_transcript "OTTHUMT00000316187.2"; +chr22 HAVANA exon 18138428 18138598 . + . gene_id "ENSG00000099968.13"; transcript_id "ENST00000493680.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BCL2L13"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BCL2L13-004"; exon_number 2; exon_id "ENSE00003647715.1"; level 2; protein_id "ENSP00000434764.1"; tag "alternative_5_UTR"; tag "basic"; havana_gene "OTTHUMG00000150088.3"; havana_transcript "OTTHUMT00000316187.2"; +chr22 HAVANA CDS 18138478 18138598 . + 0 gene_id "ENSG00000099968.13"; transcript_id "ENST00000493680.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BCL2L13"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BCL2L13-004"; exon_number 2; exon_id "ENSE00003647715.1"; level 2; protein_id "ENSP00000434764.1"; tag "alternative_5_UTR"; tag "basic"; havana_gene "OTTHUMG00000150088.3"; havana_transcript "OTTHUMT00000316187.2"; +chr22 HAVANA start_codon 18138478 18138480 . + 0 gene_id "ENSG00000099968.13"; transcript_id "ENST00000493680.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BCL2L13"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BCL2L13-004"; exon_number 2; exon_id "ENSE00003647715.1"; level 2; protein_id "ENSP00000434764.1"; tag "alternative_5_UTR"; tag "basic"; havana_gene "OTTHUMG00000150088.3"; havana_transcript "OTTHUMT00000316187.2"; +chr22 HAVANA exon 18165980 18166087 . + . gene_id "ENSG00000099968.13"; transcript_id "ENST00000493680.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BCL2L13"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BCL2L13-004"; exon_number 3; exon_id "ENSE00003693073.1"; level 2; protein_id "ENSP00000434764.1"; tag "alternative_5_UTR"; tag "basic"; havana_gene "OTTHUMG00000150088.3"; havana_transcript "OTTHUMT00000316187.2"; +chr22 HAVANA CDS 18165980 18166087 . + 2 gene_id "ENSG00000099968.13"; transcript_id "ENST00000493680.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BCL2L13"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BCL2L13-004"; exon_number 3; exon_id "ENSE00003693073.1"; level 2; protein_id "ENSP00000434764.1"; tag "alternative_5_UTR"; tag "basic"; havana_gene "OTTHUMG00000150088.3"; havana_transcript "OTTHUMT00000316187.2"; +chr22 HAVANA exon 18171752 18171908 . + . gene_id "ENSG00000099968.13"; transcript_id "ENST00000493680.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BCL2L13"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BCL2L13-004"; exon_number 4; exon_id "ENSE00003591214.1"; level 2; protein_id "ENSP00000434764.1"; tag "alternative_5_UTR"; tag "basic"; havana_gene "OTTHUMG00000150088.3"; havana_transcript "OTTHUMT00000316187.2"; +chr22 HAVANA CDS 18171752 18171908 . + 2 gene_id "ENSG00000099968.13"; transcript_id "ENST00000493680.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BCL2L13"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BCL2L13-004"; exon_number 4; exon_id "ENSE00003591214.1"; level 2; protein_id "ENSP00000434764.1"; tag "alternative_5_UTR"; tag "basic"; havana_gene "OTTHUMG00000150088.3"; havana_transcript "OTTHUMT00000316187.2"; +chr22 HAVANA exon 18178907 18178976 . + . gene_id "ENSG00000099968.13"; transcript_id "ENST00000493680.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BCL2L13"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BCL2L13-004"; exon_number 5; exon_id "ENSE00003497481.1"; level 2; protein_id "ENSP00000434764.1"; tag "alternative_5_UTR"; tag "basic"; havana_gene "OTTHUMG00000150088.3"; havana_transcript "OTTHUMT00000316187.2"; +chr22 HAVANA CDS 18178907 18178976 . + 1 gene_id "ENSG00000099968.13"; transcript_id "ENST00000493680.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BCL2L13"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BCL2L13-004"; exon_number 5; exon_id "ENSE00003497481.1"; level 2; protein_id "ENSP00000434764.1"; tag "alternative_5_UTR"; tag "basic"; havana_gene "OTTHUMG00000150088.3"; havana_transcript "OTTHUMT00000316187.2"; +chr22 HAVANA exon 18185009 18186499 . + . gene_id "ENSG00000099968.13"; transcript_id "ENST00000493680.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BCL2L13"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BCL2L13-004"; exon_number 6; exon_id "ENSE00001841813.1"; level 2; protein_id "ENSP00000434764.1"; tag "alternative_5_UTR"; tag "basic"; havana_gene "OTTHUMG00000150088.3"; havana_transcript "OTTHUMT00000316187.2"; +chr22 HAVANA CDS 18185009 18185155 . + 0 gene_id "ENSG00000099968.13"; transcript_id "ENST00000493680.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BCL2L13"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BCL2L13-004"; exon_number 6; exon_id "ENSE00001841813.1"; level 2; protein_id "ENSP00000434764.1"; tag "alternative_5_UTR"; tag "basic"; havana_gene "OTTHUMG00000150088.3"; havana_transcript "OTTHUMT00000316187.2"; +chr22 HAVANA stop_codon 18185156 18185158 . + 0 gene_id "ENSG00000099968.13"; transcript_id "ENST00000493680.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BCL2L13"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BCL2L13-004"; exon_number 6; exon_id "ENSE00001841813.1"; level 2; protein_id "ENSP00000434764.1"; tag "alternative_5_UTR"; tag "basic"; havana_gene "OTTHUMG00000150088.3"; havana_transcript "OTTHUMT00000316187.2"; +chr22 HAVANA UTR 18121538 18121652 . + . gene_id "ENSG00000099968.13"; transcript_id "ENST00000493680.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BCL2L13"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BCL2L13-004"; level 2; protein_id "ENSP00000434764.1"; tag "alternative_5_UTR"; tag "basic"; havana_gene "OTTHUMG00000150088.3"; havana_transcript "OTTHUMT00000316187.2"; +chr22 HAVANA UTR 18138428 18138477 . + . gene_id "ENSG00000099968.13"; transcript_id "ENST00000493680.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BCL2L13"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BCL2L13-004"; level 2; protein_id "ENSP00000434764.1"; tag "alternative_5_UTR"; tag "basic"; havana_gene "OTTHUMG00000150088.3"; havana_transcript "OTTHUMT00000316187.2"; +chr22 HAVANA UTR 18185156 18186499 . + . gene_id "ENSG00000099968.13"; transcript_id "ENST00000493680.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BCL2L13"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BCL2L13-004"; level 2; protein_id "ENSP00000434764.1"; tag "alternative_5_UTR"; tag "basic"; havana_gene "OTTHUMG00000150088.3"; havana_transcript "OTTHUMT00000316187.2"; +chr22 HAVANA transcript 18121577 18213388 . + . gene_id "ENSG00000099968.13"; transcript_id "ENST00000355028.3"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BCL2L13"; transcript_type "protein_coding"; transcript_status "NOVEL"; transcript_name "BCL2L13-005"; level 2; protein_id "ENSP00000347133.3"; tag "basic"; tag "CCDS"; ccdsid "CCDS59447.1"; havana_gene "OTTHUMG00000150088.3"; havana_transcript "OTTHUMT00000316188.1"; +chr22 HAVANA exon 18121577 18121652 . + . gene_id "ENSG00000099968.13"; transcript_id "ENST00000355028.3"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BCL2L13"; transcript_type "protein_coding"; transcript_status "NOVEL"; transcript_name "BCL2L13-005"; exon_number 1; exon_id "ENSE00001832778.1"; level 2; protein_id "ENSP00000347133.3"; tag "basic"; tag "CCDS"; ccdsid "CCDS59447.1"; havana_gene "OTTHUMG00000150088.3"; havana_transcript "OTTHUMT00000316188.1"; +chr22 HAVANA exon 18138428 18138598 . + . gene_id "ENSG00000099968.13"; transcript_id "ENST00000355028.3"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BCL2L13"; transcript_type "protein_coding"; transcript_status "NOVEL"; transcript_name "BCL2L13-005"; exon_number 2; exon_id "ENSE00003647715.1"; level 2; protein_id "ENSP00000347133.3"; tag "basic"; tag "CCDS"; ccdsid "CCDS59447.1"; havana_gene "OTTHUMG00000150088.3"; havana_transcript "OTTHUMT00000316188.1"; +chr22 HAVANA CDS 18138478 18138598 . + 0 gene_id "ENSG00000099968.13"; transcript_id "ENST00000355028.3"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BCL2L13"; transcript_type "protein_coding"; transcript_status "NOVEL"; transcript_name "BCL2L13-005"; exon_number 2; exon_id "ENSE00003647715.1"; level 2; protein_id "ENSP00000347133.3"; tag "basic"; tag "CCDS"; ccdsid "CCDS59447.1"; havana_gene "OTTHUMG00000150088.3"; havana_transcript "OTTHUMT00000316188.1"; +chr22 HAVANA start_codon 18138478 18138480 . + 0 gene_id "ENSG00000099968.13"; transcript_id "ENST00000355028.3"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BCL2L13"; transcript_type "protein_coding"; transcript_status "NOVEL"; transcript_name "BCL2L13-005"; exon_number 2; exon_id "ENSE00003647715.1"; level 2; protein_id "ENSP00000347133.3"; tag "basic"; tag "CCDS"; ccdsid "CCDS59447.1"; havana_gene "OTTHUMG00000150088.3"; havana_transcript "OTTHUMT00000316188.1"; +chr22 HAVANA exon 18165980 18166087 . + . gene_id "ENSG00000099968.13"; transcript_id "ENST00000355028.3"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BCL2L13"; transcript_type "protein_coding"; transcript_status "NOVEL"; transcript_name "BCL2L13-005"; exon_number 3; exon_id "ENSE00003693073.1"; level 2; protein_id "ENSP00000347133.3"; tag "basic"; tag "CCDS"; ccdsid "CCDS59447.1"; havana_gene "OTTHUMG00000150088.3"; havana_transcript "OTTHUMT00000316188.1"; +chr22 HAVANA CDS 18165980 18166087 . + 2 gene_id "ENSG00000099968.13"; transcript_id "ENST00000355028.3"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BCL2L13"; transcript_type "protein_coding"; transcript_status "NOVEL"; transcript_name "BCL2L13-005"; exon_number 3; exon_id "ENSE00003693073.1"; level 2; protein_id "ENSP00000347133.3"; tag "basic"; tag "CCDS"; ccdsid "CCDS59447.1"; havana_gene "OTTHUMG00000150088.3"; havana_transcript "OTTHUMT00000316188.1"; +chr22 HAVANA exon 18171752 18171908 . + . gene_id "ENSG00000099968.13"; transcript_id "ENST00000355028.3"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BCL2L13"; transcript_type "protein_coding"; transcript_status "NOVEL"; transcript_name "BCL2L13-005"; exon_number 4; exon_id "ENSE00003591214.1"; level 2; protein_id "ENSP00000347133.3"; tag "basic"; tag "CCDS"; ccdsid "CCDS59447.1"; havana_gene "OTTHUMG00000150088.3"; havana_transcript "OTTHUMT00000316188.1"; +chr22 HAVANA CDS 18171752 18171908 . + 2 gene_id "ENSG00000099968.13"; transcript_id "ENST00000355028.3"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BCL2L13"; transcript_type "protein_coding"; transcript_status "NOVEL"; transcript_name "BCL2L13-005"; exon_number 4; exon_id "ENSE00003591214.1"; level 2; protein_id "ENSP00000347133.3"; tag "basic"; tag "CCDS"; ccdsid "CCDS59447.1"; havana_gene "OTTHUMG00000150088.3"; havana_transcript "OTTHUMT00000316188.1"; +chr22 HAVANA exon 18209443 18213388 . + . gene_id "ENSG00000099968.13"; transcript_id "ENST00000355028.3"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BCL2L13"; transcript_type "protein_coding"; transcript_status "NOVEL"; transcript_name "BCL2L13-005"; exon_number 5; exon_id "ENSE00001890669.1"; level 2; protein_id "ENSP00000347133.3"; tag "basic"; tag "CCDS"; ccdsid "CCDS59447.1"; havana_gene "OTTHUMG00000150088.3"; havana_transcript "OTTHUMT00000316188.1"; +chr22 HAVANA CDS 18209443 18209569 . + 1 gene_id "ENSG00000099968.13"; transcript_id "ENST00000355028.3"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BCL2L13"; transcript_type "protein_coding"; transcript_status "NOVEL"; transcript_name "BCL2L13-005"; exon_number 5; exon_id "ENSE00001890669.1"; level 2; protein_id "ENSP00000347133.3"; tag "basic"; tag "CCDS"; ccdsid "CCDS59447.1"; havana_gene "OTTHUMG00000150088.3"; havana_transcript "OTTHUMT00000316188.1"; +chr22 HAVANA stop_codon 18209570 18209572 . + 0 gene_id "ENSG00000099968.13"; transcript_id "ENST00000355028.3"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BCL2L13"; transcript_type "protein_coding"; transcript_status "NOVEL"; transcript_name "BCL2L13-005"; exon_number 5; exon_id "ENSE00001890669.1"; level 2; protein_id "ENSP00000347133.3"; tag "basic"; tag "CCDS"; ccdsid "CCDS59447.1"; havana_gene "OTTHUMG00000150088.3"; havana_transcript "OTTHUMT00000316188.1"; +chr22 HAVANA UTR 18121577 18121652 . + . gene_id "ENSG00000099968.13"; transcript_id "ENST00000355028.3"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BCL2L13"; transcript_type "protein_coding"; transcript_status "NOVEL"; transcript_name "BCL2L13-005"; level 2; protein_id "ENSP00000347133.3"; tag "basic"; tag "CCDS"; ccdsid "CCDS59447.1"; havana_gene "OTTHUMG00000150088.3"; havana_transcript "OTTHUMT00000316188.1"; +chr22 HAVANA UTR 18138428 18138477 . + . gene_id "ENSG00000099968.13"; transcript_id "ENST00000355028.3"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BCL2L13"; transcript_type "protein_coding"; transcript_status "NOVEL"; transcript_name "BCL2L13-005"; level 2; protein_id "ENSP00000347133.3"; tag "basic"; tag "CCDS"; ccdsid "CCDS59447.1"; havana_gene "OTTHUMG00000150088.3"; havana_transcript "OTTHUMT00000316188.1"; +chr22 HAVANA UTR 18209570 18213388 . + . gene_id "ENSG00000099968.13"; transcript_id "ENST00000355028.3"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BCL2L13"; transcript_type "protein_coding"; transcript_status "NOVEL"; transcript_name "BCL2L13-005"; level 2; protein_id "ENSP00000347133.3"; tag "basic"; tag "CCDS"; ccdsid "CCDS59447.1"; havana_gene "OTTHUMG00000150088.3"; havana_transcript "OTTHUMT00000316188.1"; +chr22 ENSEMBL transcript 18138478 18210300 . + . gene_id "ENSG00000099968.13"; transcript_id "ENST00000418951.2"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BCL2L13"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BCL2L13-202"; level 3; protein_id "ENSP00000410019.2"; tag "basic"; tag "CCDS"; ccdsid "CCDS13746.1"; havana_gene "OTTHUMG00000150088.3"; +chr22 ENSEMBL exon 18138478 18138598 . + . gene_id "ENSG00000099968.13"; transcript_id "ENST00000418951.2"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BCL2L13"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BCL2L13-202"; exon_number 1; exon_id "ENSE00001629201.2"; level 3; protein_id "ENSP00000410019.2"; tag "basic"; tag "CCDS"; ccdsid "CCDS13746.1"; havana_gene "OTTHUMG00000150088.3"; +chr22 ENSEMBL CDS 18138478 18138598 . + 0 gene_id "ENSG00000099968.13"; transcript_id "ENST00000418951.2"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BCL2L13"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BCL2L13-202"; exon_number 1; exon_id "ENSE00001629201.2"; level 3; protein_id "ENSP00000410019.2"; tag "basic"; tag "CCDS"; ccdsid "CCDS13746.1"; havana_gene "OTTHUMG00000150088.3"; +chr22 ENSEMBL start_codon 18138478 18138480 . + 0 gene_id "ENSG00000099968.13"; transcript_id "ENST00000418951.2"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BCL2L13"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BCL2L13-202"; exon_number 1; exon_id "ENSE00001629201.2"; level 3; protein_id "ENSP00000410019.2"; tag "basic"; tag "CCDS"; ccdsid "CCDS13746.1"; havana_gene "OTTHUMG00000150088.3"; +chr22 ENSEMBL exon 18165980 18166087 . + . gene_id "ENSG00000099968.13"; transcript_id "ENST00000418951.2"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BCL2L13"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BCL2L13-202"; exon_number 2; exon_id "ENSE00003693073.1"; level 3; protein_id "ENSP00000410019.2"; tag "basic"; tag "CCDS"; ccdsid "CCDS13746.1"; havana_gene "OTTHUMG00000150088.3"; +chr22 ENSEMBL CDS 18165980 18166087 . + 2 gene_id "ENSG00000099968.13"; transcript_id "ENST00000418951.2"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BCL2L13"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BCL2L13-202"; exon_number 2; exon_id "ENSE00003693073.1"; level 3; protein_id "ENSP00000410019.2"; tag "basic"; tag "CCDS"; ccdsid "CCDS13746.1"; havana_gene "OTTHUMG00000150088.3"; +chr22 ENSEMBL exon 18167375 18167472 . + . gene_id "ENSG00000099968.13"; transcript_id "ENST00000418951.2"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BCL2L13"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BCL2L13-202"; exon_number 3; exon_id "ENSE00001315528.2"; level 3; protein_id "ENSP00000410019.2"; tag "basic"; tag "CCDS"; ccdsid "CCDS13746.1"; havana_gene "OTTHUMG00000150088.3"; +chr22 ENSEMBL CDS 18167375 18167457 . + 2 gene_id "ENSG00000099968.13"; transcript_id "ENST00000418951.2"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BCL2L13"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BCL2L13-202"; exon_number 3; exon_id "ENSE00001315528.2"; level 3; protein_id "ENSP00000410019.2"; tag "basic"; tag "CCDS"; ccdsid "CCDS13746.1"; havana_gene "OTTHUMG00000150088.3"; +chr22 ENSEMBL stop_codon 18167458 18167460 . + 0 gene_id "ENSG00000099968.13"; transcript_id "ENST00000418951.2"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BCL2L13"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BCL2L13-202"; exon_number 3; exon_id "ENSE00001315528.2"; level 3; protein_id "ENSP00000410019.2"; tag "basic"; tag "CCDS"; ccdsid "CCDS13746.1"; havana_gene "OTTHUMG00000150088.3"; +chr22 ENSEMBL exon 18171752 18171908 . + . gene_id "ENSG00000099968.13"; transcript_id "ENST00000418951.2"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BCL2L13"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BCL2L13-202"; exon_number 4; exon_id "ENSE00003687973.1"; level 3; protein_id "ENSP00000410019.2"; tag "basic"; tag "CCDS"; ccdsid "CCDS13746.1"; havana_gene "OTTHUMG00000150088.3"; +chr22 ENSEMBL exon 18209443 18210300 . + . gene_id "ENSG00000099968.13"; transcript_id "ENST00000418951.2"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BCL2L13"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BCL2L13-202"; exon_number 5; exon_id "ENSE00001540150.3"; level 3; protein_id "ENSP00000410019.2"; tag "basic"; tag "CCDS"; ccdsid "CCDS13746.1"; havana_gene "OTTHUMG00000150088.3"; +chr22 ENSEMBL UTR 18167458 18167472 . + . gene_id "ENSG00000099968.13"; transcript_id "ENST00000418951.2"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BCL2L13"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BCL2L13-202"; level 3; protein_id "ENSP00000410019.2"; tag "basic"; tag "CCDS"; ccdsid "CCDS13746.1"; havana_gene "OTTHUMG00000150088.3"; +chr22 ENSEMBL UTR 18171752 18171908 . + . gene_id "ENSG00000099968.13"; transcript_id "ENST00000418951.2"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BCL2L13"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BCL2L13-202"; level 3; protein_id "ENSP00000410019.2"; tag "basic"; tag "CCDS"; ccdsid "CCDS13746.1"; havana_gene "OTTHUMG00000150088.3"; +chr22 ENSEMBL UTR 18209443 18210300 . + . gene_id "ENSG00000099968.13"; transcript_id "ENST00000418951.2"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BCL2L13"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BCL2L13-202"; level 3; protein_id "ENSP00000410019.2"; tag "basic"; tag "CCDS"; ccdsid "CCDS13746.1"; havana_gene "OTTHUMG00000150088.3"; +chr22 HAVANA transcript 18171840 18211906 . + . gene_id "ENSG00000099968.13"; transcript_id "ENST00000399777.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BCL2L13"; transcript_type "nonsense_mediated_decay"; transcript_status "KNOWN"; transcript_name "BCL2L13-006"; level 2; protein_id "ENSP00000382677.1"; tag "mRNA_start_NF"; tag "cds_start_NF"; havana_gene "OTTHUMG00000150088.3"; havana_transcript "OTTHUMT00000316189.3"; +chr22 HAVANA exon 18171840 18171908 . + . gene_id "ENSG00000099968.13"; transcript_id "ENST00000399777.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BCL2L13"; transcript_type "nonsense_mediated_decay"; transcript_status "KNOWN"; transcript_name "BCL2L13-006"; exon_number 1; exon_id "ENSE00001540161.1"; level 2; protein_id "ENSP00000382677.1"; tag "mRNA_start_NF"; tag "cds_start_NF"; havana_gene "OTTHUMG00000150088.3"; havana_transcript "OTTHUMT00000316189.3"; +chr22 HAVANA CDS 18171840 18171908 . + 1 gene_id "ENSG00000099968.13"; transcript_id "ENST00000399777.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BCL2L13"; transcript_type "nonsense_mediated_decay"; transcript_status "KNOWN"; transcript_name "BCL2L13-006"; exon_number 1; exon_id "ENSE00001540161.1"; level 2; protein_id "ENSP00000382677.1"; tag "mRNA_start_NF"; tag "cds_start_NF"; havana_gene "OTTHUMG00000150088.3"; havana_transcript "OTTHUMT00000316189.3"; +chr22 HAVANA exon 18185009 18185152 . + . gene_id "ENSG00000099968.13"; transcript_id "ENST00000399777.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BCL2L13"; transcript_type "nonsense_mediated_decay"; transcript_status "KNOWN"; transcript_name "BCL2L13-006"; exon_number 2; exon_id "ENSE00003526121.1"; level 2; protein_id "ENSP00000382677.1"; tag "mRNA_start_NF"; tag "cds_start_NF"; havana_gene "OTTHUMG00000150088.3"; havana_transcript "OTTHUMT00000316189.3"; +chr22 HAVANA CDS 18185009 18185051 . + 1 gene_id "ENSG00000099968.13"; transcript_id "ENST00000399777.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BCL2L13"; transcript_type "nonsense_mediated_decay"; transcript_status "KNOWN"; transcript_name "BCL2L13-006"; exon_number 2; exon_id "ENSE00003526121.1"; level 2; protein_id "ENSP00000382677.1"; tag "mRNA_start_NF"; tag "cds_start_NF"; havana_gene "OTTHUMG00000150088.3"; havana_transcript "OTTHUMT00000316189.3"; +chr22 HAVANA stop_codon 18185052 18185054 . + 0 gene_id "ENSG00000099968.13"; transcript_id "ENST00000399777.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BCL2L13"; transcript_type "nonsense_mediated_decay"; transcript_status "KNOWN"; transcript_name "BCL2L13-006"; exon_number 2; exon_id "ENSE00003526121.1"; level 2; protein_id "ENSP00000382677.1"; tag "mRNA_start_NF"; tag "cds_start_NF"; havana_gene "OTTHUMG00000150088.3"; havana_transcript "OTTHUMT00000316189.3"; +chr22 HAVANA exon 18209443 18211906 . + . gene_id "ENSG00000099968.13"; transcript_id "ENST00000399777.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BCL2L13"; transcript_type "nonsense_mediated_decay"; transcript_status "KNOWN"; transcript_name "BCL2L13-006"; exon_number 3; exon_id "ENSE00001399631.3"; level 2; protein_id "ENSP00000382677.1"; tag "mRNA_start_NF"; tag "cds_start_NF"; havana_gene "OTTHUMG00000150088.3"; havana_transcript "OTTHUMT00000316189.3"; +chr22 HAVANA UTR 18185052 18185152 . + . gene_id "ENSG00000099968.13"; transcript_id "ENST00000399777.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BCL2L13"; transcript_type "nonsense_mediated_decay"; transcript_status "KNOWN"; transcript_name "BCL2L13-006"; level 2; protein_id "ENSP00000382677.1"; tag "mRNA_start_NF"; tag "cds_start_NF"; havana_gene "OTTHUMG00000150088.3"; havana_transcript "OTTHUMT00000316189.3"; +chr22 HAVANA UTR 18209443 18211906 . + . gene_id "ENSG00000099968.13"; transcript_id "ENST00000399777.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BCL2L13"; transcript_type "nonsense_mediated_decay"; transcript_status "KNOWN"; transcript_name "BCL2L13-006"; level 2; protein_id "ENSP00000382677.1"; tag "mRNA_start_NF"; tag "cds_start_NF"; havana_gene "OTTHUMG00000150088.3"; havana_transcript "OTTHUMT00000316189.3"; +chr22 HAVANA transcript 18178504 18185129 . + . gene_id "ENSG00000099968.13"; transcript_id "ENST00000479296.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BCL2L13"; transcript_type "processed_transcript"; transcript_status "PUTATIVE"; transcript_name "BCL2L13-010"; level 2; havana_gene "OTTHUMG00000150088.3"; havana_transcript "OTTHUMT00000316193.1"; +chr22 HAVANA exon 18178504 18178976 . + . gene_id "ENSG00000099968.13"; transcript_id "ENST00000479296.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BCL2L13"; transcript_type "processed_transcript"; transcript_status "PUTATIVE"; transcript_name "BCL2L13-010"; exon_number 1; exon_id "ENSE00001926348.1"; level 2; havana_gene "OTTHUMG00000150088.3"; havana_transcript "OTTHUMT00000316193.1"; +chr22 HAVANA exon 18185009 18185129 . + . gene_id "ENSG00000099968.13"; transcript_id "ENST00000479296.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BCL2L13"; transcript_type "processed_transcript"; transcript_status "PUTATIVE"; transcript_name "BCL2L13-010"; exon_number 2; exon_id "ENSE00001895448.1"; level 2; havana_gene "OTTHUMG00000150088.3"; havana_transcript "OTTHUMT00000316193.1"; +chr22 HAVANA transcript 18189476 18210436 . + . gene_id "ENSG00000099968.13"; transcript_id "ENST00000485631.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BCL2L13"; transcript_type "processed_transcript"; transcript_status "PUTATIVE"; transcript_name "BCL2L13-007"; level 1; tag "basic"; tag "exp_conf"; havana_gene "OTTHUMG00000150088.3"; havana_transcript "OTTHUMT00000316190.1"; +chr22 HAVANA exon 18189476 18189591 . + . gene_id "ENSG00000099968.13"; transcript_id "ENST00000485631.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BCL2L13"; transcript_type "processed_transcript"; transcript_status "PUTATIVE"; transcript_name "BCL2L13-007"; exon_number 1; exon_id "ENSE00001958207.1"; level 1; tag "basic"; tag "exp_conf"; havana_gene "OTTHUMG00000150088.3"; havana_transcript "OTTHUMT00000316190.1"; +chr22 HAVANA exon 18209443 18210436 . + . gene_id "ENSG00000099968.13"; transcript_id "ENST00000485631.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BCL2L13"; transcript_type "processed_transcript"; transcript_status "PUTATIVE"; transcript_name "BCL2L13-007"; exon_number 2; exon_id "ENSE00001826278.1"; level 1; tag "basic"; tag "exp_conf"; havana_gene "OTTHUMG00000150088.3"; havana_transcript "OTTHUMT00000316190.1"; +chr22 HAVANA gene 18216906 18257536 . - . gene_id "ENSG00000015475.14"; transcript_id "ENSG00000015475.14"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BID"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BID"; level 2; tag "ncRNA_host"; havana_gene "OTTHUMG00000150087.4"; +chr22 HAVANA transcript 18216906 18256782 . - . gene_id "ENSG00000015475.14"; transcript_id "ENST00000317361.7"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BID"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BID-002"; level 2; protein_id "ENSP00000318822.7"; tag "basic"; tag "CCDS"; ccdsid "CCDS13747.1"; havana_gene "OTTHUMG00000150087.4"; havana_transcript "OTTHUMT00000316179.1"; +chr22 HAVANA exon 18256376 18256782 . - . gene_id "ENSG00000015475.14"; transcript_id "ENST00000317361.7"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BID"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BID-002"; exon_number 1; exon_id "ENSE00001349079.5"; level 2; protein_id "ENSP00000318822.7"; tag "basic"; tag "CCDS"; ccdsid "CCDS13747.1"; havana_gene "OTTHUMG00000150087.4"; havana_transcript "OTTHUMT00000316179.1"; +chr22 HAVANA CDS 18256376 18256455 . - 0 gene_id "ENSG00000015475.14"; transcript_id "ENST00000317361.7"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BID"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BID-002"; exon_number 1; exon_id "ENSE00001349079.5"; level 2; protein_id "ENSP00000318822.7"; tag "basic"; tag "CCDS"; ccdsid "CCDS13747.1"; havana_gene "OTTHUMG00000150087.4"; havana_transcript "OTTHUMT00000316179.1"; +chr22 HAVANA start_codon 18256453 18256455 . - 0 gene_id "ENSG00000015475.14"; transcript_id "ENST00000317361.7"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BID"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BID-002"; exon_number 1; exon_id "ENSE00001349079.5"; level 2; protein_id "ENSP00000318822.7"; tag "basic"; tag "CCDS"; ccdsid "CCDS13747.1"; havana_gene "OTTHUMG00000150087.4"; havana_transcript "OTTHUMT00000316179.1"; +chr22 HAVANA exon 18232871 18232940 . - . gene_id "ENSG00000015475.14"; transcript_id "ENST00000317361.7"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BID"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BID-002"; exon_number 2; exon_id "ENSE00003568392.1"; level 2; protein_id "ENSP00000318822.7"; tag "basic"; tag "CCDS"; ccdsid "CCDS13747.1"; havana_gene "OTTHUMG00000150087.4"; havana_transcript "OTTHUMT00000316179.1"; +chr22 HAVANA CDS 18232871 18232940 . - 1 gene_id "ENSG00000015475.14"; transcript_id "ENST00000317361.7"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BID"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BID-002"; exon_number 2; exon_id "ENSE00003568392.1"; level 2; protein_id "ENSP00000318822.7"; tag "basic"; tag "CCDS"; ccdsid "CCDS13747.1"; havana_gene "OTTHUMG00000150087.4"; havana_transcript "OTTHUMT00000316179.1"; +chr22 HAVANA exon 18226569 18226779 . - . gene_id "ENSG00000015475.14"; transcript_id "ENST00000317361.7"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BID"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BID-002"; exon_number 3; exon_id "ENSE00003565087.1"; level 2; protein_id "ENSP00000318822.7"; tag "basic"; tag "CCDS"; ccdsid "CCDS13747.1"; havana_gene "OTTHUMG00000150087.4"; havana_transcript "OTTHUMT00000316179.1"; +chr22 HAVANA CDS 18226569 18226779 . - 0 gene_id "ENSG00000015475.14"; transcript_id "ENST00000317361.7"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BID"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BID-002"; exon_number 3; exon_id "ENSE00003565087.1"; level 2; protein_id "ENSP00000318822.7"; tag "basic"; tag "CCDS"; ccdsid "CCDS13747.1"; havana_gene "OTTHUMG00000150087.4"; havana_transcript "OTTHUMT00000316179.1"; +chr22 HAVANA exon 18222115 18222254 . - . gene_id "ENSG00000015475.14"; transcript_id "ENST00000317361.7"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BID"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BID-002"; exon_number 4; exon_id "ENSE00003689682.1"; level 2; protein_id "ENSP00000318822.7"; tag "basic"; tag "CCDS"; ccdsid "CCDS13747.1"; havana_gene "OTTHUMG00000150087.4"; havana_transcript "OTTHUMT00000316179.1"; +chr22 HAVANA CDS 18222115 18222254 . - 2 gene_id "ENSG00000015475.14"; transcript_id "ENST00000317361.7"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BID"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BID-002"; exon_number 4; exon_id "ENSE00003689682.1"; level 2; protein_id "ENSP00000318822.7"; tag "basic"; tag "CCDS"; ccdsid "CCDS13747.1"; havana_gene "OTTHUMG00000150087.4"; havana_transcript "OTTHUMT00000316179.1"; +chr22 HAVANA exon 18220783 18220995 . - . gene_id "ENSG00000015475.14"; transcript_id "ENST00000317361.7"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BID"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BID-002"; exon_number 5; exon_id "ENSE00003542752.1"; level 2; protein_id "ENSP00000318822.7"; tag "basic"; tag "CCDS"; ccdsid "CCDS13747.1"; havana_gene "OTTHUMG00000150087.4"; havana_transcript "OTTHUMT00000316179.1"; +chr22 HAVANA CDS 18220783 18220995 . - 0 gene_id "ENSG00000015475.14"; transcript_id "ENST00000317361.7"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BID"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BID-002"; exon_number 5; exon_id "ENSE00003542752.1"; level 2; protein_id "ENSP00000318822.7"; tag "basic"; tag "CCDS"; ccdsid "CCDS13747.1"; havana_gene "OTTHUMG00000150087.4"; havana_transcript "OTTHUMT00000316179.1"; +chr22 HAVANA exon 18216906 18218357 . - . gene_id "ENSG00000015475.14"; transcript_id "ENST00000317361.7"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BID"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BID-002"; exon_number 6; exon_id "ENSE00001946765.1"; level 2; protein_id "ENSP00000318822.7"; tag "basic"; tag "CCDS"; ccdsid "CCDS13747.1"; havana_gene "OTTHUMG00000150087.4"; havana_transcript "OTTHUMT00000316179.1"; +chr22 HAVANA CDS 18218349 18218357 . - 0 gene_id "ENSG00000015475.14"; transcript_id "ENST00000317361.7"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BID"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BID-002"; exon_number 6; exon_id "ENSE00001946765.1"; level 2; protein_id "ENSP00000318822.7"; tag "basic"; tag "CCDS"; ccdsid "CCDS13747.1"; havana_gene "OTTHUMG00000150087.4"; havana_transcript "OTTHUMT00000316179.1"; +chr22 HAVANA stop_codon 18218346 18218348 . - 0 gene_id "ENSG00000015475.14"; transcript_id "ENST00000317361.7"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BID"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BID-002"; exon_number 6; exon_id "ENSE00001946765.1"; level 2; protein_id "ENSP00000318822.7"; tag "basic"; tag "CCDS"; ccdsid "CCDS13747.1"; havana_gene "OTTHUMG00000150087.4"; havana_transcript "OTTHUMT00000316179.1"; +chr22 HAVANA UTR 18256456 18256782 . - . gene_id "ENSG00000015475.14"; transcript_id "ENST00000317361.7"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BID"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BID-002"; level 2; protein_id "ENSP00000318822.7"; tag "basic"; tag "CCDS"; ccdsid "CCDS13747.1"; havana_gene "OTTHUMG00000150087.4"; havana_transcript "OTTHUMT00000316179.1"; +chr22 HAVANA UTR 18216906 18218348 . - . gene_id "ENSG00000015475.14"; transcript_id "ENST00000317361.7"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BID"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BID-002"; level 2; protein_id "ENSP00000318822.7"; tag "basic"; tag "CCDS"; ccdsid "CCDS13747.1"; havana_gene "OTTHUMG00000150087.4"; havana_transcript "OTTHUMT00000316179.1"; +chr22 ENSEMBL transcript 18216908 18257258 . - . gene_id "ENSG00000015475.14"; transcript_id "ENST00000399767.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BID"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BID-201"; level 3; protein_id "ENSP00000382669.1"; tag "basic"; tag "CCDS"; ccdsid "CCDS13749.1"; havana_gene "OTTHUMG00000150087.4"; +chr22 ENSEMBL exon 18257147 18257258 . - . gene_id "ENSG00000015475.14"; transcript_id "ENST00000399767.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BID"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BID-201"; exon_number 1; exon_id "ENSE00001540140.1"; level 3; protein_id "ENSP00000382669.1"; tag "basic"; tag "CCDS"; ccdsid "CCDS13749.1"; havana_gene "OTTHUMG00000150087.4"; +chr22 ENSEMBL exon 18226569 18226779 . - . gene_id "ENSG00000015475.14"; transcript_id "ENST00000399767.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BID"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BID-201"; exon_number 2; exon_id "ENSE00003489267.1"; level 3; protein_id "ENSP00000382669.1"; tag "basic"; tag "CCDS"; ccdsid "CCDS13749.1"; havana_gene "OTTHUMG00000150087.4"; +chr22 ENSEMBL exon 18222115 18222254 . - . gene_id "ENSG00000015475.14"; transcript_id "ENST00000399767.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BID"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BID-201"; exon_number 3; exon_id "ENSE00003616197.1"; level 3; protein_id "ENSP00000382669.1"; tag "basic"; tag "CCDS"; ccdsid "CCDS13749.1"; havana_gene "OTTHUMG00000150087.4"; +chr22 ENSEMBL CDS 18222115 18222189 . - 0 gene_id "ENSG00000015475.14"; transcript_id "ENST00000399767.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BID"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BID-201"; exon_number 3; exon_id "ENSE00003616197.1"; level 3; protein_id "ENSP00000382669.1"; tag "basic"; tag "CCDS"; ccdsid "CCDS13749.1"; havana_gene "OTTHUMG00000150087.4"; +chr22 ENSEMBL start_codon 18222187 18222189 . - 0 gene_id "ENSG00000015475.14"; transcript_id "ENST00000399767.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BID"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BID-201"; exon_number 3; exon_id "ENSE00003616197.1"; level 3; protein_id "ENSP00000382669.1"; tag "basic"; tag "CCDS"; ccdsid "CCDS13749.1"; havana_gene "OTTHUMG00000150087.4"; +chr22 ENSEMBL exon 18220783 18220995 . - . gene_id "ENSG00000015475.14"; transcript_id "ENST00000399767.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BID"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BID-201"; exon_number 4; exon_id "ENSE00003542752.1"; level 3; protein_id "ENSP00000382669.1"; tag "basic"; tag "CCDS"; ccdsid "CCDS13749.1"; havana_gene "OTTHUMG00000150087.4"; +chr22 ENSEMBL CDS 18220783 18220995 . - 0 gene_id "ENSG00000015475.14"; transcript_id "ENST00000399767.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BID"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BID-201"; exon_number 4; exon_id "ENSE00003542752.1"; level 3; protein_id "ENSP00000382669.1"; tag "basic"; tag "CCDS"; ccdsid "CCDS13749.1"; havana_gene "OTTHUMG00000150087.4"; +chr22 ENSEMBL exon 18216908 18218357 . - . gene_id "ENSG00000015475.14"; transcript_id "ENST00000399767.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BID"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BID-201"; exon_number 5; exon_id "ENSE00001389825.1"; level 3; protein_id "ENSP00000382669.1"; tag "basic"; tag "CCDS"; ccdsid "CCDS13749.1"; havana_gene "OTTHUMG00000150087.4"; +chr22 ENSEMBL CDS 18218349 18218357 . - 0 gene_id "ENSG00000015475.14"; transcript_id "ENST00000399767.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BID"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BID-201"; exon_number 5; exon_id "ENSE00001389825.1"; level 3; protein_id "ENSP00000382669.1"; tag "basic"; tag "CCDS"; ccdsid "CCDS13749.1"; havana_gene "OTTHUMG00000150087.4"; +chr22 ENSEMBL stop_codon 18218346 18218348 . - 0 gene_id "ENSG00000015475.14"; transcript_id "ENST00000399767.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BID"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BID-201"; exon_number 5; exon_id "ENSE00001389825.1"; level 3; protein_id "ENSP00000382669.1"; tag "basic"; tag "CCDS"; ccdsid "CCDS13749.1"; havana_gene "OTTHUMG00000150087.4"; +chr22 ENSEMBL UTR 18257147 18257258 . - . gene_id "ENSG00000015475.14"; transcript_id "ENST00000399767.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BID"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BID-201"; level 3; protein_id "ENSP00000382669.1"; tag "basic"; tag "CCDS"; ccdsid "CCDS13749.1"; havana_gene "OTTHUMG00000150087.4"; +chr22 ENSEMBL UTR 18226569 18226779 . - . gene_id "ENSG00000015475.14"; transcript_id "ENST00000399767.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BID"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BID-201"; level 3; protein_id "ENSP00000382669.1"; tag "basic"; tag "CCDS"; ccdsid "CCDS13749.1"; havana_gene "OTTHUMG00000150087.4"; +chr22 ENSEMBL UTR 18222190 18222254 . - . gene_id "ENSG00000015475.14"; transcript_id "ENST00000399767.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BID"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BID-201"; level 3; protein_id "ENSP00000382669.1"; tag "basic"; tag "CCDS"; ccdsid "CCDS13749.1"; havana_gene "OTTHUMG00000150087.4"; +chr22 ENSEMBL UTR 18216908 18218348 . - . gene_id "ENSG00000015475.14"; transcript_id "ENST00000399767.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BID"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BID-201"; level 3; protein_id "ENSP00000382669.1"; tag "basic"; tag "CCDS"; ccdsid "CCDS13749.1"; havana_gene "OTTHUMG00000150087.4"; +chr22 HAVANA transcript 18216937 18257258 . - . gene_id "ENSG00000015475.14"; transcript_id "ENST00000399774.3"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BID"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BID-001"; level 2; protein_id "ENSP00000382674.3"; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS13748.1"; havana_gene "OTTHUMG00000150087.4"; havana_transcript "OTTHUMT00000316178.1"; +chr22 HAVANA exon 18257147 18257258 . - . gene_id "ENSG00000015475.14"; transcript_id "ENST00000399774.3"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BID"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BID-001"; exon_number 1; exon_id "ENSE00001540140.1"; level 2; protein_id "ENSP00000382674.3"; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS13748.1"; havana_gene "OTTHUMG00000150087.4"; havana_transcript "OTTHUMT00000316178.1"; +chr22 HAVANA exon 18232871 18232940 . - . gene_id "ENSG00000015475.14"; transcript_id "ENST00000399774.3"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BID"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BID-001"; exon_number 2; exon_id "ENSE00003526724.1"; level 2; protein_id "ENSP00000382674.3"; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS13748.1"; havana_gene "OTTHUMG00000150087.4"; havana_transcript "OTTHUMT00000316178.1"; +chr22 HAVANA CDS 18232871 18232882 . - 0 gene_id "ENSG00000015475.14"; transcript_id "ENST00000399774.3"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BID"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BID-001"; exon_number 2; exon_id "ENSE00003526724.1"; level 2; protein_id "ENSP00000382674.3"; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS13748.1"; havana_gene "OTTHUMG00000150087.4"; havana_transcript "OTTHUMT00000316178.1"; +chr22 HAVANA start_codon 18232880 18232882 . - 0 gene_id "ENSG00000015475.14"; transcript_id "ENST00000399774.3"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BID"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BID-001"; exon_number 2; exon_id "ENSE00003526724.1"; level 2; protein_id "ENSP00000382674.3"; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS13748.1"; havana_gene "OTTHUMG00000150087.4"; havana_transcript "OTTHUMT00000316178.1"; +chr22 HAVANA exon 18226569 18226779 . - . gene_id "ENSG00000015475.14"; transcript_id "ENST00000399774.3"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BID"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BID-001"; exon_number 3; exon_id "ENSE00003565087.1"; level 2; protein_id "ENSP00000382674.3"; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS13748.1"; havana_gene "OTTHUMG00000150087.4"; havana_transcript "OTTHUMT00000316178.1"; +chr22 HAVANA CDS 18226569 18226779 . - 0 gene_id "ENSG00000015475.14"; transcript_id "ENST00000399774.3"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BID"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BID-001"; exon_number 3; exon_id "ENSE00003565087.1"; level 2; protein_id "ENSP00000382674.3"; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS13748.1"; havana_gene "OTTHUMG00000150087.4"; havana_transcript "OTTHUMT00000316178.1"; +chr22 HAVANA exon 18222115 18222254 . - . gene_id "ENSG00000015475.14"; transcript_id "ENST00000399774.3"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BID"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BID-001"; exon_number 4; exon_id "ENSE00003689682.1"; level 2; protein_id "ENSP00000382674.3"; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS13748.1"; havana_gene "OTTHUMG00000150087.4"; havana_transcript "OTTHUMT00000316178.1"; +chr22 HAVANA CDS 18222115 18222254 . - 2 gene_id "ENSG00000015475.14"; transcript_id "ENST00000399774.3"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BID"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BID-001"; exon_number 4; exon_id "ENSE00003689682.1"; level 2; protein_id "ENSP00000382674.3"; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS13748.1"; havana_gene "OTTHUMG00000150087.4"; havana_transcript "OTTHUMT00000316178.1"; +chr22 HAVANA exon 18220783 18220995 . - . gene_id "ENSG00000015475.14"; transcript_id "ENST00000399774.3"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BID"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BID-001"; exon_number 5; exon_id "ENSE00003542752.1"; level 2; protein_id "ENSP00000382674.3"; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS13748.1"; havana_gene "OTTHUMG00000150087.4"; havana_transcript "OTTHUMT00000316178.1"; +chr22 HAVANA CDS 18220783 18220995 . - 0 gene_id "ENSG00000015475.14"; transcript_id "ENST00000399774.3"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BID"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BID-001"; exon_number 5; exon_id "ENSE00003542752.1"; level 2; protein_id "ENSP00000382674.3"; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS13748.1"; havana_gene "OTTHUMG00000150087.4"; havana_transcript "OTTHUMT00000316178.1"; +chr22 HAVANA exon 18216937 18218357 . - . gene_id "ENSG00000015475.14"; transcript_id "ENST00000399774.3"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BID"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BID-001"; exon_number 6; exon_id "ENSE00001856820.1"; level 2; protein_id "ENSP00000382674.3"; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS13748.1"; havana_gene "OTTHUMG00000150087.4"; havana_transcript "OTTHUMT00000316178.1"; +chr22 HAVANA CDS 18218349 18218357 . - 0 gene_id "ENSG00000015475.14"; transcript_id "ENST00000399774.3"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BID"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BID-001"; exon_number 6; exon_id "ENSE00001856820.1"; level 2; protein_id "ENSP00000382674.3"; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS13748.1"; havana_gene "OTTHUMG00000150087.4"; havana_transcript "OTTHUMT00000316178.1"; +chr22 HAVANA stop_codon 18218346 18218348 . - 0 gene_id "ENSG00000015475.14"; transcript_id "ENST00000399774.3"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BID"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BID-001"; exon_number 6; exon_id "ENSE00001856820.1"; level 2; protein_id "ENSP00000382674.3"; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS13748.1"; havana_gene "OTTHUMG00000150087.4"; havana_transcript "OTTHUMT00000316178.1"; +chr22 HAVANA UTR 18257147 18257258 . - . gene_id "ENSG00000015475.14"; transcript_id "ENST00000399774.3"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BID"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BID-001"; level 2; protein_id "ENSP00000382674.3"; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS13748.1"; havana_gene "OTTHUMG00000150087.4"; havana_transcript "OTTHUMT00000316178.1"; +chr22 HAVANA UTR 18232883 18232940 . - . gene_id "ENSG00000015475.14"; transcript_id "ENST00000399774.3"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BID"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BID-001"; level 2; protein_id "ENSP00000382674.3"; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS13748.1"; havana_gene "OTTHUMG00000150087.4"; havana_transcript "OTTHUMT00000316178.1"; +chr22 HAVANA UTR 18216937 18218348 . - . gene_id "ENSG00000015475.14"; transcript_id "ENST00000399774.3"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BID"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BID-001"; level 2; protein_id "ENSP00000382674.3"; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS13748.1"; havana_gene "OTTHUMG00000150087.4"; havana_transcript "OTTHUMT00000316178.1"; +chr22 HAVANA transcript 18216941 18257255 . - . gene_id "ENSG00000015475.14"; transcript_id "ENST00000399765.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BID"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BID-004"; level 2; protein_id "ENSP00000382667.1"; tag "basic"; tag "CCDS"; ccdsid "CCDS13749.1"; havana_gene "OTTHUMG00000150087.4"; havana_transcript "OTTHUMT00000316181.1"; +chr22 HAVANA exon 18257147 18257255 . - . gene_id "ENSG00000015475.14"; transcript_id "ENST00000399765.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BID"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BID-004"; exon_number 1; exon_id "ENSE00001540096.1"; level 2; protein_id "ENSP00000382667.1"; tag "basic"; tag "CCDS"; ccdsid "CCDS13749.1"; havana_gene "OTTHUMG00000150087.4"; havana_transcript "OTTHUMT00000316181.1"; +chr22 HAVANA exon 18222115 18222254 . - . gene_id "ENSG00000015475.14"; transcript_id "ENST00000399765.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BID"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BID-004"; exon_number 2; exon_id "ENSE00003616197.1"; level 2; protein_id "ENSP00000382667.1"; tag "basic"; tag "CCDS"; ccdsid "CCDS13749.1"; havana_gene "OTTHUMG00000150087.4"; havana_transcript "OTTHUMT00000316181.1"; +chr22 HAVANA CDS 18222115 18222189 . - 0 gene_id "ENSG00000015475.14"; transcript_id "ENST00000399765.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BID"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BID-004"; exon_number 2; exon_id "ENSE00003616197.1"; level 2; protein_id "ENSP00000382667.1"; tag "basic"; tag "CCDS"; ccdsid "CCDS13749.1"; havana_gene "OTTHUMG00000150087.4"; havana_transcript "OTTHUMT00000316181.1"; +chr22 HAVANA start_codon 18222187 18222189 . - 0 gene_id "ENSG00000015475.14"; transcript_id "ENST00000399765.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BID"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BID-004"; exon_number 2; exon_id "ENSE00003616197.1"; level 2; protein_id "ENSP00000382667.1"; tag "basic"; tag "CCDS"; ccdsid "CCDS13749.1"; havana_gene "OTTHUMG00000150087.4"; havana_transcript "OTTHUMT00000316181.1"; +chr22 HAVANA exon 18220783 18220995 . - . gene_id "ENSG00000015475.14"; transcript_id "ENST00000399765.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BID"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BID-004"; exon_number 3; exon_id "ENSE00003542752.1"; level 2; protein_id "ENSP00000382667.1"; tag "basic"; tag "CCDS"; ccdsid "CCDS13749.1"; havana_gene "OTTHUMG00000150087.4"; havana_transcript "OTTHUMT00000316181.1"; +chr22 HAVANA CDS 18220783 18220995 . - 0 gene_id "ENSG00000015475.14"; transcript_id "ENST00000399765.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BID"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BID-004"; exon_number 3; exon_id "ENSE00003542752.1"; level 2; protein_id "ENSP00000382667.1"; tag "basic"; tag "CCDS"; ccdsid "CCDS13749.1"; havana_gene "OTTHUMG00000150087.4"; havana_transcript "OTTHUMT00000316181.1"; +chr22 HAVANA exon 18216941 18218357 . - . gene_id "ENSG00000015475.14"; transcript_id "ENST00000399765.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BID"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BID-004"; exon_number 4; exon_id "ENSE00001540093.1"; level 2; protein_id "ENSP00000382667.1"; tag "basic"; tag "CCDS"; ccdsid "CCDS13749.1"; havana_gene "OTTHUMG00000150087.4"; havana_transcript "OTTHUMT00000316181.1"; +chr22 HAVANA CDS 18218349 18218357 . - 0 gene_id "ENSG00000015475.14"; transcript_id "ENST00000399765.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BID"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BID-004"; exon_number 4; exon_id "ENSE00001540093.1"; level 2; protein_id "ENSP00000382667.1"; tag "basic"; tag "CCDS"; ccdsid "CCDS13749.1"; havana_gene "OTTHUMG00000150087.4"; havana_transcript "OTTHUMT00000316181.1"; +chr22 HAVANA stop_codon 18218346 18218348 . - 0 gene_id "ENSG00000015475.14"; transcript_id "ENST00000399765.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BID"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BID-004"; exon_number 4; exon_id "ENSE00001540093.1"; level 2; protein_id "ENSP00000382667.1"; tag "basic"; tag "CCDS"; ccdsid "CCDS13749.1"; havana_gene "OTTHUMG00000150087.4"; havana_transcript "OTTHUMT00000316181.1"; +chr22 HAVANA UTR 18257147 18257255 . - . gene_id "ENSG00000015475.14"; transcript_id "ENST00000399765.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BID"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BID-004"; level 2; protein_id "ENSP00000382667.1"; tag "basic"; tag "CCDS"; ccdsid "CCDS13749.1"; havana_gene "OTTHUMG00000150087.4"; havana_transcript "OTTHUMT00000316181.1"; +chr22 HAVANA UTR 18222190 18222254 . - . gene_id "ENSG00000015475.14"; transcript_id "ENST00000399765.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BID"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BID-004"; level 2; protein_id "ENSP00000382667.1"; tag "basic"; tag "CCDS"; ccdsid "CCDS13749.1"; havana_gene "OTTHUMG00000150087.4"; havana_transcript "OTTHUMT00000316181.1"; +chr22 HAVANA UTR 18216941 18218348 . - . gene_id "ENSG00000015475.14"; transcript_id "ENST00000399765.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BID"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BID-004"; level 2; protein_id "ENSP00000382667.1"; tag "basic"; tag "CCDS"; ccdsid "CCDS13749.1"; havana_gene "OTTHUMG00000150087.4"; havana_transcript "OTTHUMT00000316181.1"; +chr22 HAVANA transcript 18217988 18223960 . - . gene_id "ENSG00000015475.14"; transcript_id "ENST00000494097.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BID"; transcript_type "retained_intron"; transcript_status "KNOWN"; transcript_name "BID-005"; level 2; havana_gene "OTTHUMG00000150087.4"; havana_transcript "OTTHUMT00000316182.1"; +chr22 HAVANA exon 18222115 18223960 . - . gene_id "ENSG00000015475.14"; transcript_id "ENST00000494097.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BID"; transcript_type "retained_intron"; transcript_status "KNOWN"; transcript_name "BID-005"; exon_number 1; exon_id "ENSE00001855408.1"; level 2; havana_gene "OTTHUMG00000150087.4"; havana_transcript "OTTHUMT00000316182.1"; +chr22 HAVANA exon 18220783 18220995 . - . gene_id "ENSG00000015475.14"; transcript_id "ENST00000494097.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BID"; transcript_type "retained_intron"; transcript_status "KNOWN"; transcript_name "BID-005"; exon_number 2; exon_id "ENSE00003683851.1"; level 2; havana_gene "OTTHUMG00000150087.4"; havana_transcript "OTTHUMT00000316182.1"; +chr22 HAVANA exon 18217988 18218357 . - . gene_id "ENSG00000015475.14"; transcript_id "ENST00000494097.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BID"; transcript_type "retained_intron"; transcript_status "KNOWN"; transcript_name "BID-005"; exon_number 3; exon_id "ENSE00001892438.1"; level 2; havana_gene "OTTHUMG00000150087.4"; havana_transcript "OTTHUMT00000316182.1"; +chr22 HAVANA transcript 18218265 18257178 . - . gene_id "ENSG00000015475.14"; transcript_id "ENST00000342111.5"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BID"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BID-003"; level 2; protein_id "ENSP00000344594.5"; tag "NMD_exception"; tag "basic"; havana_gene "OTTHUMG00000150087.4"; havana_transcript "OTTHUMT00000316180.3"; +chr22 HAVANA exon 18257147 18257178 . - . gene_id "ENSG00000015475.14"; transcript_id "ENST00000342111.5"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BID"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BID-003"; exon_number 1; exon_id "ENSE00002195037.1"; level 2; protein_id "ENSP00000344594.5"; tag "NMD_exception"; tag "basic"; havana_gene "OTTHUMG00000150087.4"; havana_transcript "OTTHUMT00000316180.3"; +chr22 HAVANA exon 18232871 18232940 . - . gene_id "ENSG00000015475.14"; transcript_id "ENST00000342111.5"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BID"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BID-003"; exon_number 2; exon_id "ENSE00003526724.1"; level 2; protein_id "ENSP00000344594.5"; tag "NMD_exception"; tag "basic"; havana_gene "OTTHUMG00000150087.4"; havana_transcript "OTTHUMT00000316180.3"; +chr22 HAVANA CDS 18232871 18232882 . - 0 gene_id "ENSG00000015475.14"; transcript_id "ENST00000342111.5"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BID"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BID-003"; exon_number 2; exon_id "ENSE00003526724.1"; level 2; protein_id "ENSP00000344594.5"; tag "NMD_exception"; tag "basic"; havana_gene "OTTHUMG00000150087.4"; havana_transcript "OTTHUMT00000316180.3"; +chr22 HAVANA start_codon 18232880 18232882 . - 0 gene_id "ENSG00000015475.14"; transcript_id "ENST00000342111.5"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BID"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BID-003"; exon_number 2; exon_id "ENSE00003526724.1"; level 2; protein_id "ENSP00000344594.5"; tag "NMD_exception"; tag "basic"; havana_gene "OTTHUMG00000150087.4"; havana_transcript "OTTHUMT00000316180.3"; +chr22 HAVANA exon 18226569 18226779 . - . gene_id "ENSG00000015475.14"; transcript_id "ENST00000342111.5"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BID"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BID-003"; exon_number 3; exon_id "ENSE00003565087.1"; level 2; protein_id "ENSP00000344594.5"; tag "NMD_exception"; tag "basic"; havana_gene "OTTHUMG00000150087.4"; havana_transcript "OTTHUMT00000316180.3"; +chr22 HAVANA CDS 18226569 18226779 . - 0 gene_id "ENSG00000015475.14"; transcript_id "ENST00000342111.5"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BID"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BID-003"; exon_number 3; exon_id "ENSE00003565087.1"; level 2; protein_id "ENSP00000344594.5"; tag "NMD_exception"; tag "basic"; havana_gene "OTTHUMG00000150087.4"; havana_transcript "OTTHUMT00000316180.3"; +chr22 HAVANA exon 18222848 18222942 . - . gene_id "ENSG00000015475.14"; transcript_id "ENST00000342111.5"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BID"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BID-003"; exon_number 4; exon_id "ENSE00001374791.1"; level 2; protein_id "ENSP00000344594.5"; tag "NMD_exception"; tag "basic"; havana_gene "OTTHUMG00000150087.4"; havana_transcript "OTTHUMT00000316180.3"; +chr22 HAVANA CDS 18222848 18222942 . - 2 gene_id "ENSG00000015475.14"; transcript_id "ENST00000342111.5"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BID"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BID-003"; exon_number 4; exon_id "ENSE00001374791.1"; level 2; protein_id "ENSP00000344594.5"; tag "NMD_exception"; tag "basic"; havana_gene "OTTHUMG00000150087.4"; havana_transcript "OTTHUMT00000316180.3"; +chr22 HAVANA exon 18222115 18222254 . - . gene_id "ENSG00000015475.14"; transcript_id "ENST00000342111.5"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BID"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BID-003"; exon_number 5; exon_id "ENSE00003668564.1"; level 2; protein_id "ENSP00000344594.5"; tag "NMD_exception"; tag "basic"; havana_gene "OTTHUMG00000150087.4"; havana_transcript "OTTHUMT00000316180.3"; +chr22 HAVANA CDS 18222162 18222254 . - 0 gene_id "ENSG00000015475.14"; transcript_id "ENST00000342111.5"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BID"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BID-003"; exon_number 5; exon_id "ENSE00003668564.1"; level 2; protein_id "ENSP00000344594.5"; tag "NMD_exception"; tag "basic"; havana_gene "OTTHUMG00000150087.4"; havana_transcript "OTTHUMT00000316180.3"; +chr22 HAVANA stop_codon 18222159 18222161 . - 0 gene_id "ENSG00000015475.14"; transcript_id "ENST00000342111.5"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BID"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BID-003"; exon_number 5; exon_id "ENSE00003668564.1"; level 2; protein_id "ENSP00000344594.5"; tag "NMD_exception"; tag "basic"; havana_gene "OTTHUMG00000150087.4"; havana_transcript "OTTHUMT00000316180.3"; +chr22 HAVANA exon 18220783 18220995 . - . gene_id "ENSG00000015475.14"; transcript_id "ENST00000342111.5"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BID"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BID-003"; exon_number 6; exon_id "ENSE00003683851.1"; level 2; protein_id "ENSP00000344594.5"; tag "NMD_exception"; tag "basic"; havana_gene "OTTHUMG00000150087.4"; havana_transcript "OTTHUMT00000316180.3"; +chr22 HAVANA exon 18218265 18218357 . - . gene_id "ENSG00000015475.14"; transcript_id "ENST00000342111.5"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BID"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BID-003"; exon_number 7; exon_id "ENSE00001428765.1"; level 2; protein_id "ENSP00000344594.5"; tag "NMD_exception"; tag "basic"; havana_gene "OTTHUMG00000150087.4"; havana_transcript "OTTHUMT00000316180.3"; +chr22 HAVANA UTR 18257147 18257178 . - . gene_id "ENSG00000015475.14"; transcript_id "ENST00000342111.5"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BID"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BID-003"; level 2; protein_id "ENSP00000344594.5"; tag "NMD_exception"; tag "basic"; havana_gene "OTTHUMG00000150087.4"; havana_transcript "OTTHUMT00000316180.3"; +chr22 HAVANA UTR 18232883 18232940 . - . gene_id "ENSG00000015475.14"; transcript_id "ENST00000342111.5"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BID"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BID-003"; level 2; protein_id "ENSP00000344594.5"; tag "NMD_exception"; tag "basic"; havana_gene "OTTHUMG00000150087.4"; havana_transcript "OTTHUMT00000316180.3"; +chr22 HAVANA UTR 18222115 18222161 . - . gene_id "ENSG00000015475.14"; transcript_id "ENST00000342111.5"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BID"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BID-003"; level 2; protein_id "ENSP00000344594.5"; tag "NMD_exception"; tag "basic"; havana_gene "OTTHUMG00000150087.4"; havana_transcript "OTTHUMT00000316180.3"; +chr22 HAVANA UTR 18220783 18220995 . - . gene_id "ENSG00000015475.14"; transcript_id "ENST00000342111.5"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BID"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BID-003"; level 2; protein_id "ENSP00000344594.5"; tag "NMD_exception"; tag "basic"; havana_gene "OTTHUMG00000150087.4"; havana_transcript "OTTHUMT00000316180.3"; +chr22 HAVANA UTR 18218265 18218357 . - . gene_id "ENSG00000015475.14"; transcript_id "ENST00000342111.5"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BID"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BID-003"; level 2; protein_id "ENSP00000344594.5"; tag "NMD_exception"; tag "basic"; havana_gene "OTTHUMG00000150087.4"; havana_transcript "OTTHUMT00000316180.3"; +chr22 HAVANA transcript 18218318 18257178 . - . gene_id "ENSG00000015475.14"; transcript_id "ENST00000550946.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BID"; transcript_type "retained_intron"; transcript_status "KNOWN"; transcript_name "BID-011"; level 2; havana_gene "OTTHUMG00000150087.4"; havana_transcript "OTTHUMT00000404246.1"; +chr22 HAVANA exon 18257147 18257178 . - . gene_id "ENSG00000015475.14"; transcript_id "ENST00000550946.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BID"; transcript_type "retained_intron"; transcript_status "KNOWN"; transcript_name "BID-011"; exon_number 1; exon_id "ENSE00002195037.1"; level 2; havana_gene "OTTHUMG00000150087.4"; havana_transcript "OTTHUMT00000404246.1"; +chr22 HAVANA exon 18232871 18232940 . - . gene_id "ENSG00000015475.14"; transcript_id "ENST00000550946.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BID"; transcript_type "retained_intron"; transcript_status "KNOWN"; transcript_name "BID-011"; exon_number 2; exon_id "ENSE00003590401.1"; level 2; havana_gene "OTTHUMG00000150087.4"; havana_transcript "OTTHUMT00000404246.1"; +chr22 HAVANA exon 18226569 18226779 . - . gene_id "ENSG00000015475.14"; transcript_id "ENST00000550946.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BID"; transcript_type "retained_intron"; transcript_status "KNOWN"; transcript_name "BID-011"; exon_number 3; exon_id "ENSE00003489267.1"; level 2; havana_gene "OTTHUMG00000150087.4"; havana_transcript "OTTHUMT00000404246.1"; +chr22 HAVANA exon 18222115 18222942 . - . gene_id "ENSG00000015475.14"; transcript_id "ENST00000550946.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BID"; transcript_type "retained_intron"; transcript_status "KNOWN"; transcript_name "BID-011"; exon_number 4; exon_id "ENSE00002394631.1"; level 2; havana_gene "OTTHUMG00000150087.4"; havana_transcript "OTTHUMT00000404246.1"; +chr22 HAVANA exon 18220783 18220995 . - . gene_id "ENSG00000015475.14"; transcript_id "ENST00000550946.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BID"; transcript_type "retained_intron"; transcript_status "KNOWN"; transcript_name "BID-011"; exon_number 5; exon_id "ENSE00003683851.1"; level 2; havana_gene "OTTHUMG00000150087.4"; havana_transcript "OTTHUMT00000404246.1"; +chr22 HAVANA exon 18218318 18218357 . - . gene_id "ENSG00000015475.14"; transcript_id "ENST00000550946.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BID"; transcript_type "retained_intron"; transcript_status "KNOWN"; transcript_name "BID-011"; exon_number 6; exon_id "ENSE00003539371.1"; level 2; havana_gene "OTTHUMG00000150087.4"; havana_transcript "OTTHUMT00000404246.1"; +chr22 HAVANA transcript 18218318 18257431 . - . gene_id "ENSG00000015475.14"; transcript_id "ENST00000551952.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BID"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BID-009"; level 2; protein_id "ENSP00000449236.1"; tag "alternative_5_UTR"; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS13748.1"; havana_gene "OTTHUMG00000150087.4"; havana_transcript "OTTHUMT00000404247.1"; +chr22 HAVANA exon 18257406 18257431 . - . gene_id "ENSG00000015475.14"; transcript_id "ENST00000551952.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BID"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BID-009"; exon_number 1; exon_id "ENSE00002343949.1"; level 2; protein_id "ENSP00000449236.1"; tag "alternative_5_UTR"; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS13748.1"; havana_gene "OTTHUMG00000150087.4"; havana_transcript "OTTHUMT00000404247.1"; +chr22 HAVANA exon 18232871 18232940 . - . gene_id "ENSG00000015475.14"; transcript_id "ENST00000551952.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BID"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BID-009"; exon_number 2; exon_id "ENSE00003526724.1"; level 2; protein_id "ENSP00000449236.1"; tag "alternative_5_UTR"; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS13748.1"; havana_gene "OTTHUMG00000150087.4"; havana_transcript "OTTHUMT00000404247.1"; +chr22 HAVANA CDS 18232871 18232882 . - 0 gene_id "ENSG00000015475.14"; transcript_id "ENST00000551952.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BID"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BID-009"; exon_number 2; exon_id "ENSE00003526724.1"; level 2; protein_id "ENSP00000449236.1"; tag "alternative_5_UTR"; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS13748.1"; havana_gene "OTTHUMG00000150087.4"; havana_transcript "OTTHUMT00000404247.1"; +chr22 HAVANA start_codon 18232880 18232882 . - 0 gene_id "ENSG00000015475.14"; transcript_id "ENST00000551952.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BID"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BID-009"; exon_number 2; exon_id "ENSE00003526724.1"; level 2; protein_id "ENSP00000449236.1"; tag "alternative_5_UTR"; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS13748.1"; havana_gene "OTTHUMG00000150087.4"; havana_transcript "OTTHUMT00000404247.1"; +chr22 HAVANA exon 18226569 18226779 . - . gene_id "ENSG00000015475.14"; transcript_id "ENST00000551952.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BID"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BID-009"; exon_number 3; exon_id "ENSE00003565087.1"; level 2; protein_id "ENSP00000449236.1"; tag "alternative_5_UTR"; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS13748.1"; havana_gene "OTTHUMG00000150087.4"; havana_transcript "OTTHUMT00000404247.1"; +chr22 HAVANA CDS 18226569 18226779 . - 0 gene_id "ENSG00000015475.14"; transcript_id "ENST00000551952.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BID"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BID-009"; exon_number 3; exon_id "ENSE00003565087.1"; level 2; protein_id "ENSP00000449236.1"; tag "alternative_5_UTR"; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS13748.1"; havana_gene "OTTHUMG00000150087.4"; havana_transcript "OTTHUMT00000404247.1"; +chr22 HAVANA exon 18222115 18222254 . - . gene_id "ENSG00000015475.14"; transcript_id "ENST00000551952.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BID"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BID-009"; exon_number 4; exon_id "ENSE00003689682.1"; level 2; protein_id "ENSP00000449236.1"; tag "alternative_5_UTR"; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS13748.1"; havana_gene "OTTHUMG00000150087.4"; havana_transcript "OTTHUMT00000404247.1"; +chr22 HAVANA CDS 18222115 18222254 . - 2 gene_id "ENSG00000015475.14"; transcript_id "ENST00000551952.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BID"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BID-009"; exon_number 4; exon_id "ENSE00003689682.1"; level 2; protein_id "ENSP00000449236.1"; tag "alternative_5_UTR"; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS13748.1"; havana_gene "OTTHUMG00000150087.4"; havana_transcript "OTTHUMT00000404247.1"; +chr22 HAVANA exon 18220783 18220995 . - . gene_id "ENSG00000015475.14"; transcript_id "ENST00000551952.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BID"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BID-009"; exon_number 5; exon_id "ENSE00003542752.1"; level 2; protein_id "ENSP00000449236.1"; tag "alternative_5_UTR"; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS13748.1"; havana_gene "OTTHUMG00000150087.4"; havana_transcript "OTTHUMT00000404247.1"; +chr22 HAVANA CDS 18220783 18220995 . - 0 gene_id "ENSG00000015475.14"; transcript_id "ENST00000551952.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BID"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BID-009"; exon_number 5; exon_id "ENSE00003542752.1"; level 2; protein_id "ENSP00000449236.1"; tag "alternative_5_UTR"; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS13748.1"; havana_gene "OTTHUMG00000150087.4"; havana_transcript "OTTHUMT00000404247.1"; +chr22 HAVANA exon 18218318 18218357 . - . gene_id "ENSG00000015475.14"; transcript_id "ENST00000551952.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BID"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BID-009"; exon_number 6; exon_id "ENSE00003487532.1"; level 2; protein_id "ENSP00000449236.1"; tag "alternative_5_UTR"; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS13748.1"; havana_gene "OTTHUMG00000150087.4"; havana_transcript "OTTHUMT00000404247.1"; +chr22 HAVANA CDS 18218349 18218357 . - 0 gene_id "ENSG00000015475.14"; transcript_id "ENST00000551952.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BID"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BID-009"; exon_number 6; exon_id "ENSE00003487532.1"; level 2; protein_id "ENSP00000449236.1"; tag "alternative_5_UTR"; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS13748.1"; havana_gene "OTTHUMG00000150087.4"; havana_transcript "OTTHUMT00000404247.1"; +chr22 HAVANA stop_codon 18218346 18218348 . - 0 gene_id "ENSG00000015475.14"; transcript_id "ENST00000551952.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BID"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BID-009"; exon_number 6; exon_id "ENSE00003487532.1"; level 2; protein_id "ENSP00000449236.1"; tag "alternative_5_UTR"; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS13748.1"; havana_gene "OTTHUMG00000150087.4"; havana_transcript "OTTHUMT00000404247.1"; +chr22 HAVANA UTR 18257406 18257431 . - . gene_id "ENSG00000015475.14"; transcript_id "ENST00000551952.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BID"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BID-009"; level 2; protein_id "ENSP00000449236.1"; tag "alternative_5_UTR"; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS13748.1"; havana_gene "OTTHUMG00000150087.4"; havana_transcript "OTTHUMT00000404247.1"; +chr22 HAVANA UTR 18232883 18232940 . - . gene_id "ENSG00000015475.14"; transcript_id "ENST00000551952.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BID"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BID-009"; level 2; protein_id "ENSP00000449236.1"; tag "alternative_5_UTR"; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS13748.1"; havana_gene "OTTHUMG00000150087.4"; havana_transcript "OTTHUMT00000404247.1"; +chr22 HAVANA UTR 18218318 18218348 . - . gene_id "ENSG00000015475.14"; transcript_id "ENST00000551952.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BID"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "BID-009"; level 2; protein_id "ENSP00000449236.1"; tag "alternative_5_UTR"; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS13748.1"; havana_gene "OTTHUMG00000150087.4"; havana_transcript "OTTHUMT00000404247.1"; +chr22 HAVANA transcript 18220824 18257261 . - . gene_id "ENSG00000015475.14"; transcript_id "ENST00000473439.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BID"; transcript_type "processed_transcript"; transcript_status "PUTATIVE"; transcript_name "BID-006"; level 2; tag "basic"; havana_gene "OTTHUMG00000150087.4"; havana_transcript "OTTHUMT00000316183.1"; +chr22 HAVANA exon 18257147 18257261 . - . gene_id "ENSG00000015475.14"; transcript_id "ENST00000473439.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BID"; transcript_type "processed_transcript"; transcript_status "PUTATIVE"; transcript_name "BID-006"; exon_number 1; exon_id "ENSE00001917930.1"; level 2; tag "basic"; havana_gene "OTTHUMG00000150087.4"; havana_transcript "OTTHUMT00000316183.1"; +chr22 HAVANA exon 18226569 18226779 . - . gene_id "ENSG00000015475.14"; transcript_id "ENST00000473439.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BID"; transcript_type "processed_transcript"; transcript_status "PUTATIVE"; transcript_name "BID-006"; exon_number 2; exon_id "ENSE00003489267.1"; level 2; tag "basic"; havana_gene "OTTHUMG00000150087.4"; havana_transcript "OTTHUMT00000316183.1"; +chr22 HAVANA exon 18222115 18222254 . - . gene_id "ENSG00000015475.14"; transcript_id "ENST00000473439.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BID"; transcript_type "processed_transcript"; transcript_status "PUTATIVE"; transcript_name "BID-006"; exon_number 3; exon_id "ENSE00003500448.1"; level 2; tag "basic"; havana_gene "OTTHUMG00000150087.4"; havana_transcript "OTTHUMT00000316183.1"; +chr22 HAVANA exon 18220824 18220995 . - . gene_id "ENSG00000015475.14"; transcript_id "ENST00000473439.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BID"; transcript_type "processed_transcript"; transcript_status "PUTATIVE"; transcript_name "BID-006"; exon_number 4; exon_id "ENSE00001877316.1"; level 2; tag "basic"; havana_gene "OTTHUMG00000150087.4"; havana_transcript "OTTHUMT00000316183.1"; +chr22 HAVANA transcript 18222214 18257536 . - . gene_id "ENSG00000015475.14"; transcript_id "ENST00000552886.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BID"; transcript_type "processed_transcript"; transcript_status "KNOWN"; transcript_name "BID-008"; level 2; havana_gene "OTTHUMG00000150087.4"; havana_transcript "OTTHUMT00000404248.1"; +chr22 HAVANA exon 18257459 18257536 . - . gene_id "ENSG00000015475.14"; transcript_id "ENST00000552886.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BID"; transcript_type "processed_transcript"; transcript_status "KNOWN"; transcript_name "BID-008"; exon_number 1; exon_id "ENSE00002385433.1"; level 2; havana_gene "OTTHUMG00000150087.4"; havana_transcript "OTTHUMT00000404248.1"; +chr22 HAVANA exon 18226569 18226779 . - . gene_id "ENSG00000015475.14"; transcript_id "ENST00000552886.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BID"; transcript_type "processed_transcript"; transcript_status "KNOWN"; transcript_name "BID-008"; exon_number 2; exon_id "ENSE00003489267.1"; level 2; havana_gene "OTTHUMG00000150087.4"; havana_transcript "OTTHUMT00000404248.1"; +chr22 HAVANA exon 18222214 18222254 . - . gene_id "ENSG00000015475.14"; transcript_id "ENST00000552886.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "BID"; transcript_type "processed_transcript"; transcript_status "KNOWN"; transcript_name "BID-008"; exon_number 3; exon_id "ENSE00002342528.1"; level 2; havana_gene "OTTHUMG00000150087.4"; havana_transcript "OTTHUMT00000404248.1"; +chr22 HAVANA gene 29454660 29457832 . - . gene_id "ENSG00000100249.4"; transcript_id "ENSG00000100249.4"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "C22orf31"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "C22orf31"; level 2; havana_gene "OTTHUMG00000151011.1"; +chr22 HAVANA transcript 29454660 29457832 . - . gene_id "ENSG00000100249.4"; transcript_id "ENST00000216071.4"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "C22orf31"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "C22orf31-001"; level 2; protein_id "ENSP00000216071.4"; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS13848.1"; havana_gene "OTTHUMG00000151011.1"; havana_transcript "OTTHUMT00000320952.1"; +chr22 HAVANA exon 29457778 29457832 . - . gene_id "ENSG00000100249.4"; transcript_id "ENST00000216071.4"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "C22orf31"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "C22orf31-001"; exon_number 1; exon_id "ENSE00001048193.2"; level 2; protein_id "ENSP00000216071.4"; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS13848.1"; havana_gene "OTTHUMG00000151011.1"; havana_transcript "OTTHUMT00000320952.1"; +chr22 HAVANA CDS 29457778 29457780 . - 0 gene_id "ENSG00000100249.4"; transcript_id "ENST00000216071.4"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "C22orf31"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "C22orf31-001"; exon_number 1; exon_id "ENSE00001048193.2"; level 2; protein_id "ENSP00000216071.4"; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS13848.1"; havana_gene "OTTHUMG00000151011.1"; havana_transcript "OTTHUMT00000320952.1"; +chr22 HAVANA start_codon 29457778 29457780 . - 0 gene_id "ENSG00000100249.4"; transcript_id "ENST00000216071.4"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "C22orf31"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "C22orf31-001"; exon_number 1; exon_id "ENSE00001048193.2"; level 2; protein_id "ENSP00000216071.4"; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS13848.1"; havana_gene "OTTHUMG00000151011.1"; havana_transcript "OTTHUMT00000320952.1"; +chr22 HAVANA exon 29456403 29456831 . - . gene_id "ENSG00000100249.4"; transcript_id "ENST00000216071.4"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "C22orf31"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "C22orf31-001"; exon_number 2; exon_id "ENSE00000651998.1"; level 2; protein_id "ENSP00000216071.4"; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS13848.1"; havana_gene "OTTHUMG00000151011.1"; havana_transcript "OTTHUMT00000320952.1"; +chr22 HAVANA CDS 29456403 29456831 . - 0 gene_id "ENSG00000100249.4"; transcript_id "ENST00000216071.4"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "C22orf31"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "C22orf31-001"; exon_number 2; exon_id "ENSE00000651998.1"; level 2; protein_id "ENSP00000216071.4"; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS13848.1"; havana_gene "OTTHUMG00000151011.1"; havana_transcript "OTTHUMT00000320952.1"; +chr22 HAVANA exon 29454660 29455170 . - . gene_id "ENSG00000100249.4"; transcript_id "ENST00000216071.4"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "C22orf31"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "C22orf31-001"; exon_number 3; exon_id "ENSE00000879699.1"; level 2; protein_id "ENSP00000216071.4"; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS13848.1"; havana_gene "OTTHUMG00000151011.1"; havana_transcript "OTTHUMT00000320952.1"; +chr22 HAVANA CDS 29454733 29455170 . - 0 gene_id "ENSG00000100249.4"; transcript_id "ENST00000216071.4"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "C22orf31"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "C22orf31-001"; exon_number 3; exon_id "ENSE00000879699.1"; level 2; protein_id "ENSP00000216071.4"; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS13848.1"; havana_gene "OTTHUMG00000151011.1"; havana_transcript "OTTHUMT00000320952.1"; +chr22 HAVANA stop_codon 29454730 29454732 . - 0 gene_id "ENSG00000100249.4"; transcript_id "ENST00000216071.4"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "C22orf31"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "C22orf31-001"; exon_number 3; exon_id "ENSE00000879699.1"; level 2; protein_id "ENSP00000216071.4"; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS13848.1"; havana_gene "OTTHUMG00000151011.1"; havana_transcript "OTTHUMT00000320952.1"; +chr22 HAVANA UTR 29457781 29457832 . - . gene_id "ENSG00000100249.4"; transcript_id "ENST00000216071.4"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "C22orf31"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "C22orf31-001"; level 2; protein_id "ENSP00000216071.4"; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS13848.1"; havana_gene "OTTHUMG00000151011.1"; havana_transcript "OTTHUMT00000320952.1"; +chr22 HAVANA UTR 29454660 29454732 . - . gene_id "ENSG00000100249.4"; transcript_id "ENST00000216071.4"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "C22orf31"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "C22orf31-001"; level 2; protein_id "ENSP00000216071.4"; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS13848.1"; havana_gene "OTTHUMG00000151011.1"; havana_transcript "OTTHUMT00000320952.1"; diff --git a/scripts/importer/tests/data/manta.vcf b/scripts/importer/tests/data/manta.vcf new file mode 100644 index 000000000..ee7221f73 --- /dev/null +++ b/scripts/importer/tests/data/manta.vcf @@ -0,0 +1,19 @@ +##fileformat=VCFv4.1 +##source=SVDB +##ALT= +##ALT= +##ALT= +##ALT= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##FORMAT= +#CHROM POS ID REF ALT QUAL FILTER INFO +1 10546 cluster_14774 N N[7:159128729[ . PASS SVTYPE=BND;NSAMPLES=997;OCC=1;FRQ=0.00101300902708 +1 10549 cluster_15023 N N[18:10613[ . PASS SVTYPE=BND;NSAMPLES=997;OCC=1;FRQ=0.00101300902708 diff --git a/scripts/importer/tests/data/mates_reference.txt b/scripts/importer/tests/data/mates_reference.txt new file mode 100644 index 000000000..82ae0f13b --- /dev/null +++ b/scripts/importer/tests/data/mates_reference.txt @@ -0,0 +1,8 @@ + chrom_id | pos | ref | alt | chrom | mate_chrom | mate_start | mate_id | allele_freq | variant_id | allele_count | allele_num +---------------+-----------+-----+-----+-------+------------+------------+---------------+-------------+------------------------------+--------------+------------ + cluster_14774 | 10546 | N | N | 1 | 7 | 159128729 | | 0.00101301 | 1-10546-N-N[7:159128729[ | 0 | 0 + | 159128729 | N | N | 7 | 1 | 10546 | cluster_14774 | 0.00101301 | 7-159128729-N-N[7:159128729[ | 0 | 0 + cluster_15023 | 10549 | N | N | 1 | 18 | 10613 | | 0.00101301 | 1-10549-N-N[18:10613[ | 0 | 0 + | 10613 | N | N | 18 | 1 | 10549 | cluster_15023 | 0.00101301 | 18-10613-N-N[18:10613[ | 0 | 0 +(4 rows) + diff --git a/scripts/importer/tests/data/reference.psql b/scripts/importer/tests/data/reference.psql new file mode 100644 index 000000000..79cf7fd97 --- /dev/null +++ b/scripts/importer/tests/data/reference.psql @@ -0,0 +1,749 @@ +COPY beacon.beacon_dataset_counts_table (datasetid, dataset, callcount, variantcount) FROM stdin; +GRCh37p13:Dataset 1:Version 1 \N 18 18 +GRCh37p13:Dataset 2:Version 1 \N 12 17 +\. +COPY data.collections (id, study_name, ethnicity) FROM stdin; +1 reg undefined +2 reg undefined +\. +COPY data.studies (id, pi_name, pi_email, contact_name, contact_email, title, study_description, publication_date, ref_doi) FROM stdin; +1 name email name email SweGen \N 2001-01-01 00:00:00 doi +2 name2 email2 name2 email2 SweGen2 \N 2001-01-02 00:00:00 doi +\. +COPY data.datasets (id, study, short_name, full_name, browser_uri, beacon_uri, beacon_description, avg_seq_depth, seq_type, seq_tech, seq_center, dataset_size) FROM stdin; +1 1 Dataset 1 Dataset 1 url \N \N 0 type method place 0 +2 2 Dataset 2 Dataset 2 url \N \N 0 type method place 0 +\. +COPY data.reference_sets (id, reference_build, reference_name, ensembl_version, gencode_version, dbnsfp_version) FROM stdin; +1 GRCh37p13 GRCh37p13 homo_sapiens_core_75_37 19 2.9.3 +\. +COPY data.dataset_versions (id, dataset, reference_set, dataset_version, dataset_description, terms, available_from, ref_doi, data_contact_name, data_contact_link, num_variants, coverage_levels, portal_avail, file_access, beacon_access) FROM stdin; +1 1 1 Version 1 desc terms 2001-01-01 00:00:00 doi place email 18 {1,5,10,15,20,25,30,50,100} t REGISTERED PUBLIC +2 1 1 Version 2 desc terms 2001-01-02 00:00:00 doi place email 12 {1,5,10,15,20,25,30,50,100} t REGISTERED PUBLIC +3 2 1 Version 1 desc terms 2001-01-02 00:00:00 doi place email 12 {1,5,10,15,20,25,30,50,100} t REGISTERED PUBLIC +\. +COPY data.coverage (id, dataset_version, chrom, pos, mean, median, coverage) FROM stdin; +1 1 22 46515890 37.8400002 37 {1,1,1,1,0.99000001,0.959999979,0.860000014,0.0799999982,0} +2 1 22 46515900 38.0200005 37 {1,1,1,1,0.99000001,0.970000029,0.850000024,0.0799999982,0} +3 1 22 46515910 37.9700012 38 {1,1,1,1,0.99000001,0.959999979,0.850000024,0.0900000036,0} +4 1 22 46515920 38.2700005 38 {1,1,1,1,0.99000001,0.959999979,0.870000005,0.0799999982,0} +5 1 22 46515930 38.4000015 38 {1,1,1,1,0.99000001,0.959999979,0.860000014,0.100000001,0} +6 1 22 46515940 38.5299988 38 {1,1,1,1,1,0.949999988,0.870000005,0.100000001,0} +7 1 22 46515950 38.0499992 38 {1,1,1,1,0.99000001,0.939999998,0.870000005,0.109999999,0} +8 1 22 46515960 37.9900017 37 {1,1,1,1,1,0.949999988,0.850000024,0.119999997,0} +9 1 22 46515970 37.9000015 37 {1,1,1,1,0.99000001,0.959999979,0.860000014,0.109999999,0} +10 1 22 46515980 37.4900017 37 {1,1,1,1,0.99000001,0.930000007,0.850000024,0.0900000036,0} +11 1 22 46515990 37.9099998 37 {1,1,1,1,0.99000001,0.949999988,0.829999983,0.100000001,0} +12 1 22 46516000 37.6300011 37 {1,1,1,1,0.99000001,0.949999988,0.819999993,0.100000001,0} +13 1 22 46516010 37.7000008 37 {1,1,1,1,0.99000001,0.949999988,0.829999983,0.0900000036,0} +14 1 22 46516020 37.6300011 37 {1,1,1,1,0.99000001,0.949999988,0.839999974,0.0900000036,0} +15 1 22 46516030 37.8800011 37 {1,1,1,1,0.99000001,0.959999979,0.860000014,0.0799999982,0} +16 1 22 46516040 37.0600014 36 {1,1,1,1,0.99000001,0.939999998,0.829999983,0.0700000003,0} +17 1 22 46516050 36.3400002 36 {1,1,1,1,0.99000001,0.930000007,0.800000012,0.0599999987,0} +18 1 22 46516060 36.2799988 36 {1,1,1,1,0.99000001,0.930000007,0.800000012,0.0599999987,0} +19 1 22 46516070 35.8600006 35 {1,1,1,1,0.99000001,0.939999998,0.779999971,0.0599999987,0} +20 1 22 46516080 35.3800011 35 {1,1,1,1,0.99000001,0.939999998,0.779999971,0.0599999987,0} +21 1 22 46516090 35.1899986 34 {1,1,1,1,0.99000001,0.930000007,0.75999999,0.0599999987,0} +22 1 22 46516100 34.8800011 34 {1,1,1,1,1,0.920000017,0.75,0.0399999991,0} +23 1 22 46516110 35.1399994 35 {1,1,1,1,0.99000001,0.920000017,0.779999971,0.0500000007,0} +24 1 22 46516120 35.2000008 34 {1,1,1,1,1,0.939999998,0.790000021,0.0500000007,0} +25 1 22 46516130 35.2799988 35 {1,1,1,1,0.99000001,0.930000007,0.75999999,0.0500000007,0} +26 2 22 16364820 75.4499969 71 {1,1,0.999000013,0.998000026,0.998000026,0.994000018,0.976000011,0.792999983,0.170000002} +27 2 22 16364830 75.9400024 71 {1,1,0.999000013,0.999000013,0.998000026,0.994000018,0.977999985,0.801999986,0.179000005} +28 2 22 16364840 74.8899994 70 {1,1,1,0.999000013,0.996999979,0.991999984,0.976999998,0.791999996,0.166999996} +29 2 22 16364850 72.9400024 69 {1,1,0.999000013,0.999000013,0.996999979,0.991999984,0.976000011,0.772000015,0.157000005} +30 2 22 16364860 71.0599976 67 {1,1,0.999000013,0.999000013,0.996999979,0.987999976,0.973999977,0.762000024,0.143999994} +31 2 22 16364870 67.4100037 63 {1,1,0.999000013,0.998000026,0.996999979,0.986999989,0.968999982,0.722000003,0.112000003} +32 2 22 16364880 64.2600021 60 {1,1,1,0.998000026,0.994000018,0.986999989,0.958000004,0.693000019,0.0799999982} +33 2 22 16364890 60.9199982 58 {1,1,1,0.998000026,0.995000005,0.986000001,0.957000017,0.637000024,0.0560000017} +34 2 22 16364900 58.8899994 56 {1,1,1,0.998000026,0.995000005,0.98299998,0.953000009,0.611999989,0.0419999994} +35 2 22 16364910 57.5699997 54 {1,1,1,0.996999979,0.994000018,0.98299998,0.94599998,0.589999974,0.0370000005} +36 2 22 16364920 56.25 53.5 {1,1,1,0.995999992,0.990999997,0.98299998,0.938000023,0.57099998,0.0299999993} +37 2 22 16364930 55.1800003 53 {1,1,1,0.995999992,0.990999997,0.980000019,0.944000006,0.546999991,0.0250000004} +38 2 22 16364940 55.1500015 53 {1,1,1,0.996999979,0.990999997,0.976999998,0.954999983,0.555999994,0.0260000005} +39 2 22 16364950 54 52 {1,1,1,0.998000026,0.990999997,0.978999972,0.95599997,0.532000005,0.0189999994} +40 2 22 16364960 51.6800003 50 {1,1,1,0.995999992,0.99000001,0.976000011,0.940999985,0.476000011,0.0140000004} +41 2 22 16364970 50.6199989 48 {1,1,1,0.995999992,0.989000022,0.973999977,0.927999973,0.451000005,0.0109999999} +42 2 22 16364980 50.5 48.5 {1,1,1,0.996999979,0.99000001,0.975000024,0.93900001,0.451000005,0.00999999978} +43 2 22 16364990 50.8499985 49 {1,1,1,0.996999979,0.992999971,0.977999985,0.941999972,0.460000008,0.00999999978} +44 2 22 16365000 50.9799995 49 {1,1,1,0.998000026,0.991999984,0.981999993,0.941999972,0.453999996,0.00999999978} +45 2 22 16365010 51.2400017 49 {1,1,1,0.998000026,0.991999984,0.981999993,0.950999975,0.451999992,0.0109999999} +46 2 22 16365020 52.4599991 50 {1,1,1,0.998000026,0.991999984,0.981000006,0.957000017,0.488999993,0.00999999978} +47 2 22 16365030 52.9500008 51 {1,1,1,0.999000013,0.992999971,0.981999993,0.958999991,0.504999995,0.0109999999} +48 2 22 16365040 53.5299988 51 {1,1,1,0.998000026,0.995000005,0.986999989,0.959999979,0.521000028,0.0120000001} +\. +COPY data.dataset_files (id, dataset_version, basename, uri, file_size) FROM stdin; +\. +COPY data.dataset_logos (id, dataset, mimetype, bytes) FROM stdin; +\. +COPY data.genes (id, reference_set, gene_id, gene_name, full_name, canonical_transcript, chrom, start_pos, end_pos, strand) FROM stdin; +1 1 ENSG00000198062 POTEH POTE ankyrin domain family, member H ENST00000343518 22 16256441 16287937 - +2 1 ENSG00000236666 POTEH-AS1 \N ENST00000422014 22 16274560 16278602 + +3 1 ENSG00000226474 LA16c-2F2.5 \N ENST00000440999 22 16362385 16362561 + +4 1 ENSG00000231565 NEK2P2 NEK2 pseudogene 2 ENST00000438441 22 16364867 16366204 + +5 1 ENSG00000230471 LA16c-2F2.8 \N ENST00000428118 22 16373081 16377055 + +6 1 ENSG00000099968 BCL2L13 BCL2-like 13 (apoptosis facilitator) ENST00000317582 22 18111621 18213388 + +7 1 ENSG00000015475 BID BH3 interacting domain death agonist ENST00000317361 22 18216906 18257536 - +8 1 ENSG00000100249 C22orf31 \N ENST00000216071 22 29454660 29457832 - +\. +COPY data.transcripts (id, transcript_id, gene, mim_annotation, mim_gene_accession, chrom, start_pos, stop_pos, strand) FROM stdin; +1 ENST00000452800 1 \N \N 22 16256441 16287717 - +2 ENST00000343518 1 \N \N 22 16256441 16287937 - +3 ENST00000422014 2 \N \N 22 16274560 16278602 + +4 ENST00000440999 3 \N \N 22 16362385 16362561 + +5 ENST00000438441 4 \N \N 22 16364867 16366204 + +6 ENST00000428118 5 \N \N 22 16373081 16377055 + +7 ENST00000399781 6 \N \N 22 18111621 18178975 + +8 ENST00000399782 6 \N \N 22 18111682 18185194 + +9 ENST00000317582 6 \N \N 22 18121356 18211487 + +10 ENST00000498133 6 \N \N 22 18121507 18211465 + +11 ENST00000543133 6 \N \N 22 18121507 18211465 + +12 ENST00000464649 6 \N \N 22 18121523 18175161 + +13 ENST00000538149 6 \N \N 22 18121523 18210466 + +14 ENST00000337612 6 \N \N 22 18121530 18210428 + +15 ENST00000493680 6 \N \N 22 18121538 18186499 + +16 ENST00000355028 6 \N \N 22 18121577 18213388 + +17 ENST00000418951 6 \N \N 22 18138478 18210300 + +18 ENST00000399777 6 \N \N 22 18171840 18211906 + +19 ENST00000479296 6 \N \N 22 18178504 18185129 + +20 ENST00000485631 6 \N \N 22 18189476 18210436 + +21 ENST00000317361 7 \N \N 22 18216906 18256782 - +22 ENST00000399767 7 \N \N 22 18216908 18257258 - +23 ENST00000399774 7 \N \N 22 18216937 18257258 - +24 ENST00000399765 7 \N \N 22 18216941 18257255 - +25 ENST00000494097 7 \N \N 22 18217988 18223960 - +26 ENST00000342111 7 \N \N 22 18218265 18257178 - +27 ENST00000550946 7 \N \N 22 18218318 18257178 - +28 ENST00000551952 7 \N \N 22 18218318 18257431 - +29 ENST00000473439 7 \N \N 22 18220824 18257261 - +30 ENST00000552886 7 \N \N 22 18222214 18257536 - +31 ENST00000216071 8 \N \N 22 29454660 29457832 - +\. +COPY data.features (id, gene, transcript, chrom, start_pos, stop_pos, strand, feature_type) FROM stdin; +1 1 1 22 16287254 16287717 - exon +2 1 1 22 16287254 16287717 - CDS +3 1 1 22 16282478 16282592 - exon +4 1 1 22 16282478 16282592 - CDS +5 1 1 22 16282145 16282318 - exon +6 1 1 22 16282145 16282318 - CDS +7 1 1 22 16280334 16280589 - exon +8 1 1 22 16280434 16280589 - CDS +9 1 1 22 16279195 16279301 - exon +10 1 1 22 16277748 16277885 - exon +11 1 1 22 16275207 16275277 - exon +12 1 1 22 16269873 16269943 - exon +13 1 1 22 16268137 16268181 - exon +14 1 1 22 16266929 16267095 - exon +15 1 1 22 16258185 16258303 - exon +16 1 1 22 16256441 16256677 - exon +17 1 1 22 16280334 16280433 - UTR +18 1 1 22 16279195 16279301 - UTR +19 1 1 22 16277748 16277885 - UTR +20 1 1 22 16275207 16275277 - UTR +21 1 1 22 16269873 16269943 - UTR +22 1 1 22 16268137 16268181 - UTR +23 1 1 22 16266929 16267095 - UTR +24 1 1 22 16258185 16258303 - UTR +25 1 1 22 16256441 16256677 - UTR +26 1 2 22 16287254 16287937 - exon +27 1 2 22 16287254 16287885 - CDS +28 1 2 22 16282478 16282592 - exon +29 1 2 22 16282478 16282592 - CDS +30 1 2 22 16282145 16282318 - exon +31 1 2 22 16282145 16282318 - CDS +32 1 2 22 16279195 16279301 - exon +33 1 2 22 16279195 16279301 - CDS +34 1 2 22 16277748 16277885 - exon +35 1 2 22 16277748 16277885 - CDS +36 1 2 22 16275207 16275277 - exon +37 1 2 22 16275207 16275277 - CDS +38 1 2 22 16269873 16269943 - exon +39 1 2 22 16269873 16269943 - CDS +40 1 2 22 16268137 16268181 - exon +41 1 2 22 16268137 16268181 - CDS +42 1 2 22 16266929 16267095 - exon +43 1 2 22 16266929 16267095 - CDS +44 1 2 22 16258185 16258303 - exon +45 1 2 22 16258189 16258303 - CDS +46 1 2 22 16256441 16256677 - exon +47 1 2 22 16287886 16287937 - UTR +48 1 2 22 16258185 16258188 - UTR +49 1 2 22 16256441 16256677 - UTR +50 2 3 22 16274560 16275003 + exon +51 2 3 22 16276481 16278602 + exon +52 3 4 22 16362385 16362561 + exon +53 4 5 22 16364867 16366204 + exon +54 5 6 22 16373081 16373121 + exon +55 5 6 22 16373830 16373911 + exon +56 5 6 22 16375449 16377055 + exon +57 6 7 22 18111621 18111672 + exon +58 6 7 22 18120868 18121466 + exon +59 6 7 22 18138428 18138598 + exon +60 6 7 22 18165980 18166087 + exon +61 6 7 22 18178907 18178975 + exon +62 6 8 22 18111682 18111771 + exon +63 6 8 22 18120868 18121466 + exon +64 6 8 22 18138428 18138598 + exon +65 6 8 22 18138478 18138598 + CDS +66 6 8 22 18165980 18166087 + exon +67 6 8 22 18165980 18166087 + CDS +68 6 8 22 18171752 18171908 + exon +69 6 8 22 18171752 18171908 + CDS +70 6 8 22 18178907 18178976 + exon +71 6 8 22 18178907 18178976 + CDS +72 6 8 22 18185009 18185194 + exon +73 6 8 22 18185009 18185155 + CDS +74 6 8 22 18111682 18111771 + UTR +75 6 8 22 18120868 18121466 + UTR +76 6 8 22 18138428 18138477 + UTR +77 6 8 22 18185156 18185194 + UTR +78 6 9 22 18121356 18121652 + exon +79 6 9 22 18138428 18138598 + exon +80 6 9 22 18138478 18138598 + CDS +81 6 9 22 18165980 18166087 + exon +82 6 9 22 18165980 18166087 + CDS +83 6 9 22 18171752 18171908 + exon +84 6 9 22 18171752 18171908 + CDS +85 6 9 22 18178907 18178976 + exon +86 6 9 22 18178907 18178976 + CDS +87 6 9 22 18185009 18185152 + exon +88 6 9 22 18185009 18185152 + CDS +89 6 9 22 18209443 18211487 + exon +90 6 9 22 18209443 18210297 + CDS +91 6 9 22 18121356 18121652 + UTR +92 6 9 22 18138428 18138477 + UTR +93 6 9 22 18210298 18211487 + UTR +94 6 10 22 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11 22 18210298 18211465 + UTR +122 6 12 22 18121523 18121652 + exon +123 6 12 22 18165980 18166087 + exon +124 6 12 22 18171752 18171908 + exon +125 6 12 22 18175122 18175161 + exon +126 6 13 22 18121523 18121652 + exon +127 6 13 22 18138428 18138598 + exon +128 6 13 22 18138515 18138598 + CDS +129 6 13 22 18185009 18185152 + exon +130 6 13 22 18185009 18185152 + CDS +131 6 13 22 18209443 18210466 + exon +132 6 13 22 18209443 18210297 + CDS +133 6 13 22 18121523 18121652 + UTR +134 6 13 22 18138428 18138514 + UTR +135 6 13 22 18210298 18210466 + UTR +136 6 14 22 18121530 18121652 + exon +137 6 14 22 18138428 18138598 + exon +138 6 14 22 18165980 18166087 + exon +139 6 14 22 18185009 18185152 + exon +140 6 14 22 18185039 18185152 + CDS +141 6 14 22 18209443 18210428 + exon +142 6 14 22 18209443 18210297 + CDS +143 6 14 22 18121530 18121652 + UTR +144 6 14 22 18138428 18138598 + UTR +145 6 14 22 18165980 18166087 + UTR +146 6 14 22 18185009 18185038 + UTR +147 6 14 22 18210298 18210428 + UTR +148 6 15 22 18121538 18121652 + exon +149 6 15 22 18138428 18138598 + exon +150 6 15 22 18138478 18138598 + CDS +151 6 15 22 18165980 18166087 + exon +152 6 15 22 18165980 18166087 + CDS +153 6 15 22 18171752 18171908 + exon +154 6 15 22 18171752 18171908 + CDS +155 6 15 22 18178907 18178976 + exon +156 6 15 22 18178907 18178976 + CDS +157 6 15 22 18185009 18186499 + exon +158 6 15 22 18185009 18185155 + CDS +159 6 15 22 18121538 18121652 + UTR +160 6 15 22 18138428 18138477 + UTR +161 6 15 22 18185156 18186499 + UTR +162 6 16 22 18121577 18121652 + exon +163 6 16 22 18138428 18138598 + exon +164 6 16 22 18138478 18138598 + CDS +165 6 16 22 18165980 18166087 + exon +166 6 16 22 18165980 18166087 + CDS +167 6 16 22 18171752 18171908 + exon +168 6 16 22 18171752 18171908 + CDS +169 6 16 22 18209443 18213388 + exon +170 6 16 22 18209443 18209569 + CDS +171 6 16 22 18121577 18121652 + UTR +172 6 16 22 18138428 18138477 + UTR +173 6 16 22 18209570 18213388 + UTR +174 6 17 22 18138478 18138598 + exon +175 6 17 22 18138478 18138598 + CDS +176 6 17 22 18165980 18166087 + exon +177 6 17 22 18165980 18166087 + CDS +178 6 17 22 18167375 18167472 + exon +179 6 17 22 18167375 18167457 + CDS +180 6 17 22 18171752 18171908 + exon +181 6 17 22 18209443 18210300 + exon +182 6 17 22 18167458 18167472 + UTR +183 6 17 22 18171752 18171908 + UTR +184 6 17 22 18209443 18210300 + UTR +185 6 18 22 18171840 18171908 + exon +186 6 18 22 18171840 18171908 + CDS +187 6 18 22 18185009 18185152 + exon +188 6 18 22 18185009 18185051 + CDS +189 6 18 22 18209443 18211906 + exon +190 6 18 22 18185052 18185152 + UTR +191 6 18 22 18209443 18211906 + UTR +192 6 19 22 18178504 18178976 + exon +193 6 19 22 18185009 18185129 + exon +194 6 20 22 18189476 18189591 + exon +195 6 20 22 18209443 18210436 + exon +196 7 21 22 18256376 18256782 - exon +197 7 21 22 18256376 18256455 - CDS +198 7 21 22 18232871 18232940 - exon +199 7 21 22 18232871 18232940 - CDS +200 7 21 22 18226569 18226779 - exon +201 7 21 22 18226569 18226779 - CDS +202 7 21 22 18222115 18222254 - exon +203 7 21 22 18222115 18222254 - CDS +204 7 21 22 18220783 18220995 - exon +205 7 21 22 18220783 18220995 - CDS +206 7 21 22 18216906 18218357 - exon +207 7 21 22 18218349 18218357 - CDS +208 7 21 22 18256456 18256782 - UTR +209 7 21 22 18216906 18218348 - UTR +210 7 22 22 18257147 18257258 - exon +211 7 22 22 18226569 18226779 - exon +212 7 22 22 18222115 18222254 - exon +213 7 22 22 18222115 18222189 - CDS +214 7 22 22 18220783 18220995 - exon +215 7 22 22 18220783 18220995 - CDS +216 7 22 22 18216908 18218357 - exon +217 7 22 22 18218349 18218357 - CDS +218 7 22 22 18257147 18257258 - UTR +219 7 22 22 18226569 18226779 - UTR +220 7 22 22 18222190 18222254 - UTR +221 7 22 22 18216908 18218348 - UTR +222 7 23 22 18257147 18257258 - exon +223 7 23 22 18232871 18232940 - exon +224 7 23 22 18232871 18232882 - CDS +225 7 23 22 18226569 18226779 - exon +226 7 23 22 18226569 18226779 - CDS +227 7 23 22 18222115 18222254 - exon +228 7 23 22 18222115 18222254 - CDS +229 7 23 22 18220783 18220995 - exon +230 7 23 22 18220783 18220995 - CDS +231 7 23 22 18216937 18218357 - exon +232 7 23 22 18218349 18218357 - CDS +233 7 23 22 18257147 18257258 - UTR +234 7 23 22 18232883 18232940 - UTR +235 7 23 22 18216937 18218348 - UTR +236 7 24 22 18257147 18257255 - exon +237 7 24 22 18222115 18222254 - exon +238 7 24 22 18222115 18222189 - CDS +239 7 24 22 18220783 18220995 - exon +240 7 24 22 18220783 18220995 - CDS +241 7 24 22 18216941 18218357 - exon +242 7 24 22 18218349 18218357 - CDS +243 7 24 22 18257147 18257255 - UTR +244 7 24 22 18222190 18222254 - UTR +245 7 24 22 18216941 18218348 - UTR +246 7 25 22 18222115 18223960 - exon +247 7 25 22 18220783 18220995 - exon +248 7 25 22 18217988 18218357 - exon +249 7 26 22 18257147 18257178 - exon +250 7 26 22 18232871 18232940 - exon +251 7 26 22 18232871 18232882 - CDS +252 7 26 22 18226569 18226779 - exon +253 7 26 22 18226569 18226779 - CDS +254 7 26 22 18222848 18222942 - exon +255 7 26 22 18222848 18222942 - CDS +256 7 26 22 18222115 18222254 - exon +257 7 26 22 18222162 18222254 - CDS +258 7 26 22 18220783 18220995 - exon +259 7 26 22 18218265 18218357 - exon +260 7 26 22 18257147 18257178 - UTR +261 7 26 22 18232883 18232940 - UTR +262 7 26 22 18222115 18222161 - UTR +263 7 26 22 18220783 18220995 - UTR +264 7 26 22 18218265 18218357 - UTR +265 7 27 22 18257147 18257178 - exon +266 7 27 22 18232871 18232940 - exon +267 7 27 22 18226569 18226779 - exon +268 7 27 22 18222115 18222942 - exon +269 7 27 22 18220783 18220995 - exon +270 7 27 22 18218318 18218357 - exon +271 7 28 22 18257406 18257431 - exon +272 7 28 22 18232871 18232940 - exon +273 7 28 22 18232871 18232882 - CDS +274 7 28 22 18226569 18226779 - exon +275 7 28 22 18226569 18226779 - CDS +276 7 28 22 18222115 18222254 - exon +277 7 28 22 18222115 18222254 - CDS +278 7 28 22 18220783 18220995 - exon +279 7 28 22 18220783 18220995 - CDS +280 7 28 22 18218318 18218357 - exon +281 7 28 22 18218349 18218357 - CDS +282 7 28 22 18257406 18257431 - UTR +283 7 28 22 18232883 18232940 - UTR +284 7 28 22 18218318 18218348 - UTR +285 7 29 22 18257147 18257261 - exon +286 7 29 22 18226569 18226779 - exon +287 7 29 22 18222115 18222254 - exon +288 7 29 22 18220824 18220995 - exon +289 7 30 22 18257459 18257536 - exon +290 7 30 22 18226569 18226779 - exon +291 7 30 22 18222214 18222254 - exon +292 8 31 22 29457778 29457832 - exon +293 8 31 22 29457778 29457780 - CDS +294 8 31 22 29456403 29456831 - exon +295 8 31 22 29456403 29456831 - CDS +296 8 31 22 29454660 29455170 - exon +297 8 31 22 29454733 29455170 - CDS +298 8 31 22 29457781 29457832 - UTR +299 8 31 22 29454660 29454732 - UTR +\. +COPY data.gene_other_names (id, gene, name) FROM stdin; +1 1 POTE22 +2 1 CT104.7 +3 6 MIL1 +4 6 BCL-RAMBO +\. +COPY data.mates (id, dataset_version, chrom_id, pos, ref, alt, chrom, mate_chrom, mate_start, mate_id, allele_freq, variant_id, allele_count, allele_num) FROM stdin; +\. +COPY data.metrics (id, dataset_version, metric, mids, hist) FROM stdin; +\. +COPY data.sample_sets (id, dataset, collection, sample_size, phenotype) FROM stdin; +1 1 1 0 Undefined +2 2 1 0 Undefined +\. +COPY data.variants (id, dataset_version, variant_type, rsid, chrom, pos, ref, alt, site_quality, orig_alt_alleles, hom_count, allele_freq, filter_string, variant_id, allele_count, allele_num, quality_metrics, vep_annotations) FROM stdin; +1 1 \N \N 22 18118637 A G 212919 {22-18118637-A-G} \N 1 PASS 22-18118637-A-G 600 600 {"DP": "7320", "FS": "0", "MQ": "60", "QD": "29.98", "VQSLOD": "3.22", "MQRankSum": "-0.413", "BaseQRankSum": "1.45", "ReadPosRankSum": "0.867", "ClippingRankSum": "1.24", "InbreedingCoeff": "-0"} [{"AF": "1", "LoF": "", "TSL": "", "CCDS": "CCDS13746.1", "ENSP": "ENSP00000318883", "EXON": "", "Gene": "ENSG00000099968", "SIFT": "", "AA_AF": "", "EA_AF": "", "FLAGS": "", "HGVSc": "", "HGVSp": "", "PHENO": "", "miRNA": "", "AFR_AF": "1", "AMR_AF": "1", "APPRIS": "", "Allele": "G", "Codons": "", "EAS_AF": "1", "EUR_AF": "1", "IMPACT": "MODIFIER", "INTRON": "", "MAX_AF": "1", "PUBMED": "", "SAS_AF": "1", "SOURCE": "Ensembl", "STRAND": "1", "SYMBOL": "BCL2L13", "TREMBL": "B2RB43", "BIOTYPE": "protein_coding", "DOMAINS": "", "Feature": "ENST00000317582", "HGNC_ID": "17164", "SOMATIC": "", "UNIPARC": "UPI000004F301", "BAM_EDIT": "", "CLIN_SIG": "", "DISTANCE": "2719", "LoF_info": "", "PolyPhen": "", "USED_REF": "A", "CANONICAL": "YES", "GIVEN_REF": "A", "LoF_flags": "", "MOTIF_POS": "", "SWISSPROT": "Q9BXK5", "gnomAD_AF": "", "ALLELE_NUM": "1", "GENE_PHENO": "", "LoF_filter": "", "MOTIF_NAME": "", "Amino_acids": "", "Consequence": "upstream_gene_variant", "HGVS_OFFSET": "", "MAX_AF_POPS": "AFR&AMR&EAS&EUR&SAS", "CDS_position": "", "Feature_type": "Transcript", "HIGH_INF_POS": "", "REFSEQ_MATCH": "", "SYMBOL_SOURCE": "HGNC", "VARIANT_CLASS": "SNV", "cDNA_position": "", "gnomAD_AFR_AF": "", "gnomAD_AMR_AF": "", "gnomAD_ASJ_AF": "", "gnomAD_EAS_AF": "", "gnomAD_FIN_AF": "", "gnomAD_NFE_AF": "", "gnomAD_OTH_AF": "", "gnomAD_SAS_AF": "", "Protein_position": "", "Existing_variation": "rs4256048", "MOTIF_SCORE_CHANGE": ""}, {"AF": "1", "LoF": "", "TSL": "", "CCDS": "CCDS59448.1", "ENSP": "ENSP00000338932", "EXON": "", "Gene": "ENSG00000099968", "SIFT": "", "AA_AF": "", "EA_AF": "", "FLAGS": "", "HGVSc": "", "HGVSp": "", "PHENO": "", "miRNA": "", "AFR_AF": "1", "AMR_AF": "1", "APPRIS": "", "Allele": "G", "Codons": "", "EAS_AF": "1", "EUR_AF": "1", "IMPACT": "MODIFIER", "INTRON": "", "MAX_AF": "1", "PUBMED": "", "SAS_AF": "1", "SOURCE": "Ensembl", "STRAND": "1", "SYMBOL": "BCL2L13", "TREMBL": "", "BIOTYPE": "protein_coding", "DOMAINS": "", "Feature": "ENST00000337612", "HGNC_ID": "17164", "SOMATIC": "", "UNIPARC": "UPI00001A3E35", "BAM_EDIT": "", "CLIN_SIG": "", "DISTANCE": "2893", "LoF_info": "", "PolyPhen": "", "USED_REF": "A", "CANONICAL": "", "GIVEN_REF": "A", "LoF_flags": "", "MOTIF_POS": "", "SWISSPROT": "Q9BXK5", "gnomAD_AF": "", "ALLELE_NUM": "1", "GENE_PHENO": "", "LoF_filter": "", "MOTIF_NAME": "", "Amino_acids": "", "Consequence": "upstream_gene_variant", "HGVS_OFFSET": "", "MAX_AF_POPS": "AFR&AMR&EAS&EUR&SAS", "CDS_position": "", "Feature_type": "Transcript", "HIGH_INF_POS": "", "REFSEQ_MATCH": "", "SYMBOL_SOURCE": "HGNC", "VARIANT_CLASS": "SNV", "cDNA_position": "", "gnomAD_AFR_AF": "", "gnomAD_AMR_AF": "", "gnomAD_ASJ_AF": "", "gnomAD_EAS_AF": "", "gnomAD_FIN_AF": "", "gnomAD_NFE_AF": "", "gnomAD_OTH_AF": "", "gnomAD_SAS_AF": "", "Protein_position": "", "Existing_variation": "rs4256048", "MOTIF_SCORE_CHANGE": ""}, {"AF": "1", "LoF": "", "TSL": "", "CCDS": "CCDS59447.1", "ENSP": "ENSP00000347133", "EXON": "", "Gene": "ENSG00000099968", "SIFT": "", "AA_AF": "", "EA_AF": "", "FLAGS": "", "HGVSc": "", "HGVSp": "", "PHENO": "", "miRNA": "", "AFR_AF": "1", "AMR_AF": "1", "APPRIS": "", "Allele": "G", "Codons": "", "EAS_AF": "1", "EUR_AF": "1", "IMPACT": "MODIFIER", "INTRON": "", "MAX_AF": "1", "PUBMED": "", "SAS_AF": "1", "SOURCE": "Ensembl", "STRAND": "1", "SYMBOL": "BCL2L13", "TREMBL": "E9PDD6", "BIOTYPE": "protein_coding", "DOMAINS": "", "Feature": "ENST00000355028", "HGNC_ID": "17164", "SOMATIC": "", "UNIPARC": "UPI0000246DFE", "BAM_EDIT": "", "CLIN_SIG": "", "DISTANCE": "2940", "LoF_info": "", "PolyPhen": "", "USED_REF": "A", "CANONICAL": "", "GIVEN_REF": "A", "LoF_flags": "", "MOTIF_POS": "", "SWISSPROT": "", "gnomAD_AF": "", "ALLELE_NUM": "1", "GENE_PHENO": "", "LoF_filter": "", "MOTIF_NAME": "", "Amino_acids": "", "Consequence": "upstream_gene_variant", "HGVS_OFFSET": "", "MAX_AF_POPS": "AFR&AMR&EAS&EUR&SAS", "CDS_position": "", "Feature_type": "Transcript", "HIGH_INF_POS": "", "REFSEQ_MATCH": "", "SYMBOL_SOURCE": "HGNC", "VARIANT_CLASS": "SNV", "cDNA_position": "", "gnomAD_AFR_AF": "", "gnomAD_AMR_AF": "", "gnomAD_ASJ_AF": "", "gnomAD_EAS_AF": "", "gnomAD_FIN_AF": "", "gnomAD_NFE_AF": "", "gnomAD_OTH_AF": "", "gnomAD_SAS_AF": "", "Protein_position": "", "Existing_variation": "rs4256048", "MOTIF_SCORE_CHANGE": ""}, {"AF": "1", "LoF": "", "TSL": "", "CCDS": "", "ENSP": "", "EXON": "", "Gene": "ENSG00000099968", "SIFT": "", "AA_AF": "", "EA_AF": "", "FLAGS": "", "HGVSc": "ENST00000399781.1:n.53-2231A>G", "HGVSp": "", "PHENO": "", "miRNA": "", "AFR_AF": "1", "AMR_AF": "1", "APPRIS": "", "Allele": "G", "Codons": "", "EAS_AF": "1", "EUR_AF": "1", "IMPACT": "MODIFIER", "INTRON": "1/4", "MAX_AF": "1", "PUBMED": "", "SAS_AF": "1", "SOURCE": "Ensembl", "STRAND": "1", "SYMBOL": "BCL2L13", "TREMBL": "", "BIOTYPE": "processed_transcript", "DOMAINS": "", "Feature": "ENST00000399781", "HGNC_ID": "17164", "SOMATIC": "", "UNIPARC": "", "BAM_EDIT": "", "CLIN_SIG": "", "DISTANCE": "", "LoF_info": "", "PolyPhen": "", "USED_REF": "A", "CANONICAL": "", "GIVEN_REF": "A", "LoF_flags": "", "MOTIF_POS": "", "SWISSPROT": "", "gnomAD_AF": "", "ALLELE_NUM": "1", "GENE_PHENO": "", "LoF_filter": "", "MOTIF_NAME": "", "Amino_acids": "", "Consequence": "intron_variant&non_coding_transcript_variant", "HGVS_OFFSET": "", "MAX_AF_POPS": "AFR&AMR&EAS&EUR&SAS", "CDS_position": "", "Feature_type": "Transcript", "HIGH_INF_POS": "", "REFSEQ_MATCH": "", "SYMBOL_SOURCE": "HGNC", "VARIANT_CLASS": "SNV", "cDNA_position": "", "gnomAD_AFR_AF": "", "gnomAD_AMR_AF": "", "gnomAD_ASJ_AF": "", "gnomAD_EAS_AF": "", "gnomAD_FIN_AF": "", "gnomAD_NFE_AF": "", "gnomAD_OTH_AF": "", "gnomAD_SAS_AF": "", "Protein_position": "", "Existing_variation": "rs4256048", "MOTIF_SCORE_CHANGE": ""}, {"AF": "1", "LoF": "", "TSL": "", "CCDS": "", "ENSP": "ENSP00000382682", "EXON": "", "Gene": "ENSG00000099968", "SIFT": "", "AA_AF": "", "EA_AF": "", "FLAGS": "", "HGVSc": "ENST00000399782.1:c.-649-2231A>G", "HGVSp": "", "PHENO": "", "miRNA": "", "AFR_AF": "1", "AMR_AF": "1", "APPRIS": "", "Allele": "G", "Codons": "", "EAS_AF": "1", "EUR_AF": "1", "IMPACT": "MODIFIER", "INTRON": "1/6", "MAX_AF": "1", "PUBMED": "", "SAS_AF": "1", "SOURCE": "Ensembl", "STRAND": "1", "SYMBOL": 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"ExAC_Adj_MAF": "", "ExAC_EAS_MAF": "", "ExAC_FIN_MAF": "", "ExAC_NFE_MAF": "", "ExAC_OTH_MAF": "", "ExAC_SAS_MAF": "", "Feature_type": "Transcript", "HIGH_INF_POS": "", "SYMBOL_SOURCE": "Clone_based_vega_gene", "VARIANT_CLASS": "SNV", "cDNA_position": "", "Protein_position": "", "Existing_variation": "rs1153411", "MOTIF_SCORE_CHANGE": ""}, {"LoF": "", "TSL": "", "CCDS": "", "ENSP": "", "EXON": "1/1", "GMAF": "G:0.2520", "Gene": "ENSG00000231565", "SIFT": "", "FLAGS": "", "HGVSc": "ENST00000438441.1:n.423G>A", "HGVSp": "", "PHENO": "", "AA_MAF": "", "APPRIS": "", "Allele": "A", "Codons": "", "EA_MAF": "", "IMPACT": "MODIFIER", "INTRON": "", "PUBMED": "", "STRAND": "1", "SYMBOL": "NEK2P2", "TREMBL": "", "AFR_MAF": "A:0.9191", "AMR_MAF": "A:0.6888", "BIOTYPE": "processed_pseudogene", "DOMAINS": "", "EAS_MAF": "A:0.6895", "EUR_MAF": "A:0.6899", "Feature": "ENST00000438441", "HGNC_ID": "37816", "SAS_MAF": "A:0.6789", "SOMATIC": "", "UNIPARC": "", "CLIN_SIG": "", "DISTANCE": "", "ExAC_MAF": "", "LoF_info": "", "PolyPhen": "", "CANONICAL": "YES", "LoF_flags": "", "MOTIF_POS": "", "SWISSPROT": "", "ALLELE_NUM": "1", "GENE_PHENO": "", "LoF_filter": "", "MOTIF_NAME": "", "Amino_acids": "", "Consequence": "non_coding_transcript_exon_variant&non_coding_transcript_variant", "HGVS_OFFSET": "", "CDS_position": "", "ExAC_AFR_MAF": "", "ExAC_AMR_MAF": "", "ExAC_Adj_MAF": "", "ExAC_EAS_MAF": "", "ExAC_FIN_MAF": "", "ExAC_NFE_MAF": "", "ExAC_OTH_MAF": "", "ExAC_SAS_MAF": "", "Feature_type": "Transcript", "HIGH_INF_POS": "", "SYMBOL_SOURCE": "HGNC", "VARIANT_CLASS": "SNV", "cDNA_position": "423", "Protein_position": "", "Existing_variation": "rs1153411", "MOTIF_SCORE_CHANGE": ""}] +32 2 \N 371958062 22 16370229 G A 858332 {22-16370229-G-A} 0 0.486999989 VQSRTrancheSNP99.90to100.00 22-16370229-G-A 974 2000 {"DP": "77999", "FS": "3.256", "MQ": "32.13", "QD": "11.19", "VQSLOD": "-44.14", "MQRankSum": "-1.564", "BaseQRankSum": "-0.428", "ReadPosRankSum": "0.623", "ClippingRankSum": "0.059"} [{"LoF": "", "TSL": "", "CCDS": "", "ENSP": "", "EXON": "", "GMAF": "", "Gene": "ENSG00000231565", "SIFT": "", "FLAGS": "", "HGVSc": "", "HGVSp": "", "PHENO": "", "AA_MAF": "", "APPRIS": "", "Allele": "A", "Codons": "", "EA_MAF": "", "IMPACT": "MODIFIER", "INTRON": "", "PUBMED": "", "STRAND": "1", "SYMBOL": "NEK2P2", "TREMBL": "", "AFR_MAF": "", "AMR_MAF": "", "BIOTYPE": "processed_pseudogene", "DOMAINS": "", "EAS_MAF": "", "EUR_MAF": "", "Feature": "ENST00000438441", "HGNC_ID": "37816", "SAS_MAF": "", "SOMATIC": "", "UNIPARC": "", "CLIN_SIG": "", "DISTANCE": "4025", "ExAC_MAF": "", "LoF_info": "", "PolyPhen": "", "CANONICAL": "YES", "LoF_flags": "", "MOTIF_POS": "", "SWISSPROT": "", "ALLELE_NUM": "1", "GENE_PHENO": "", "LoF_filter": "", "MOTIF_NAME": "", "Amino_acids": "", "Consequence": "downstream_gene_variant", "HGVS_OFFSET": "", "CDS_position": "", "ExAC_AFR_MAF": "", "ExAC_AMR_MAF": "", "ExAC_Adj_MAF": "", "ExAC_EAS_MAF": "", "ExAC_FIN_MAF": "", "ExAC_NFE_MAF": "", "ExAC_OTH_MAF": "", "ExAC_SAS_MAF": "", "Feature_type": "Transcript", "HIGH_INF_POS": "", "SYMBOL_SOURCE": "HGNC", "VARIANT_CLASS": "SNV", "cDNA_position": "", "Protein_position": "", "Existing_variation": "rs371958062", "MOTIF_SCORE_CHANGE": ""}, {"LoF": "", "TSL": "", "CCDS": "", "ENSP": "", "EXON": "", "GMAF": "", "Gene": "ENSG00000230471", "SIFT": "", "FLAGS": "", "HGVSc": "", "HGVSp": "", "PHENO": "", "AA_MAF": "", "APPRIS": "", "Allele": "A", "Codons": "", "EA_MAF": "", "IMPACT": "MODIFIER", "INTRON": "", "PUBMED": "", "STRAND": "1", "SYMBOL": "LA16c-2F2.8", "TREMBL": "", "AFR_MAF": "", "AMR_MAF": "", "BIOTYPE": "lincRNA", "DOMAINS": "", "EAS_MAF": "", "EUR_MAF": "", "Feature": "ENST00000428118", "HGNC_ID": "", "SAS_MAF": "", "SOMATIC": "", "UNIPARC": "", "CLIN_SIG": "", "DISTANCE": "2852", "ExAC_MAF": "", "LoF_info": "", "PolyPhen": "", "CANONICAL": "YES", "LoF_flags": "", "MOTIF_POS": "", "SWISSPROT": "", "ALLELE_NUM": "1", "GENE_PHENO": "", "LoF_filter": "", "MOTIF_NAME": "", "Amino_acids": "", "Consequence": "upstream_gene_variant", "HGVS_OFFSET": "", "CDS_position": "", "ExAC_AFR_MAF": "", "ExAC_AMR_MAF": "", "ExAC_Adj_MAF": "", "ExAC_EAS_MAF": "", "ExAC_FIN_MAF": "", "ExAC_NFE_MAF": "", "ExAC_OTH_MAF": "", "ExAC_SAS_MAF": "", "Feature_type": "Transcript", "HIGH_INF_POS": "", "SYMBOL_SOURCE": "Clone_based_vega_gene", "VARIANT_CLASS": "SNV", "cDNA_position": "", "Protein_position": "", "Existing_variation": "rs371958062", "MOTIF_SCORE_CHANGE": ""}] +33 2 \N 783 22 29461622 G A 715011 {22-29461622-G-A} 772 0.62349999 PASS 22-29461622-G-A 1247 2000 {"DP": "36991", "FS": "0", "MQ": "60", "QD": "22.28", "VQSLOD": "22.38", "MQRankSum": "0.023", "BaseQRankSum": "2.44", "ReadPosRankSum": "0.313", "ClippingRankSum": "-0.031"} [{"LoF": "", "TSL": "", "CCDS": "CCDS13848.1", "ENSP": "ENSP00000216071", "EXON": "", "GMAF": "G:0.4289", "Gene": "ENSG00000100249", "SIFT": "", "FLAGS": "", "HGVSc": "", "HGVSp": "", "PHENO": "", "AA_MAF": "", "APPRIS": "", "Allele": "A", "Codons": "", "EA_MAF": "", "IMPACT": "MODIFIER", "INTRON": "", "PUBMED": "", "STRAND": "-1", "SYMBOL": "C22orf31", "TREMBL": "", "AFR_MAF": "A:0.5681", "AMR_MAF": "A:0.4654", "BIOTYPE": "protein_coding", "DOMAINS": "", "EAS_MAF": "A:0.5466", "EUR_MAF": "A:0.664", "Feature": "ENST00000216071", "HGNC_ID": "26931", "SAS_MAF": "A:0.5798", "SOMATIC": "", "UNIPARC": "UPI0000073FE0", "CLIN_SIG": "", "DISTANCE": "3790", "ExAC_MAF": "", "LoF_info": "", "PolyPhen": "", "CANONICAL": "YES", "LoF_flags": "", "MOTIF_POS": "", "SWISSPROT": "CV031_HUMAN", "ALLELE_NUM": "1", "GENE_PHENO": "", "LoF_filter": "", "MOTIF_NAME": "", "Amino_acids": "", "Consequence": "upstream_gene_variant", "HGVS_OFFSET": "", "CDS_position": "", "ExAC_AFR_MAF": "", "ExAC_AMR_MAF": "", "ExAC_Adj_MAF": "", "ExAC_EAS_MAF": "", "ExAC_FIN_MAF": "", "ExAC_NFE_MAF": "", "ExAC_OTH_MAF": "", "ExAC_SAS_MAF": "", "Feature_type": "Transcript", "HIGH_INF_POS": "", "SYMBOL_SOURCE": "HGNC", "VARIANT_CLASS": "SNV", "cDNA_position": "", "Protein_position": "", "Existing_variation": "rs783", "MOTIF_SCORE_CHANGE": ""}, {"LoF": "", "TSL": "", "CCDS": "", "ENSP": "", "EXON": "", "GMAF": "G:0.4289", "Gene": "", "SIFT": "", "FLAGS": "", "HGVSc": "", "HGVSp": "", "PHENO": "", "AA_MAF": "", "APPRIS": "", "Allele": "A", "Codons": "", "EA_MAF": "", "IMPACT": "MODIFIER", "INTRON": "", "PUBMED": "", "STRAND": "", "SYMBOL": "", "TREMBL": "", "AFR_MAF": "A:0.5681", "AMR_MAF": "A:0.4654", "BIOTYPE": "promoter_flanking_region", "DOMAINS": "", "EAS_MAF": "A:0.5466", "EUR_MAF": "A:0.664", "Feature": "ENSR00001731804", "HGNC_ID": "", "SAS_MAF": "A:0.5798", "SOMATIC": "", "UNIPARC": "", "CLIN_SIG": "", "DISTANCE": "", "ExAC_MAF": "", "LoF_info": "", "PolyPhen": "", "CANONICAL": "", "LoF_flags": "", "MOTIF_POS": "", "SWISSPROT": "", "ALLELE_NUM": "1", "GENE_PHENO": "", "LoF_filter": "", "MOTIF_NAME": "", "Amino_acids": "", "Consequence": "regulatory_region_variant", "HGVS_OFFSET": "", "CDS_position": "", "ExAC_AFR_MAF": "", "ExAC_AMR_MAF": "", "ExAC_Adj_MAF": "", "ExAC_EAS_MAF": "", "ExAC_FIN_MAF": "", "ExAC_NFE_MAF": "", "ExAC_OTH_MAF": "", "ExAC_SAS_MAF": "", "Feature_type": "RegulatoryFeature", "HIGH_INF_POS": "", "SYMBOL_SOURCE": "", "VARIANT_CLASS": "SNV", "cDNA_position": "", "Protein_position": "", "Existing_variation": "rs783", "MOTIF_SCORE_CHANGE": ""}] +34 3 \N 587697622 22 16050075 A G 100 {22-16050075-A-G} \N 0.000199680508 PASS 22-16050075-A-G 1 5008 {"DP": "8012"} \N +35 3 \N 587642978 22 16064513 A AAGAATGGCCTAATAC 100 {22-16064513-A-AAGAATGGCCTAATAC} \N 0.0041932906 PASS 22-16064513-A-AAGAATGGCCTAATAC 21 5008 {"DP": "26803"} \N +36 3 \N 574946654 22 16497141 CTT C 100 {22-16497141-CTT-C} \N 0.000798722031 PASS 22-16497141-CTT-C 4 5008 {"DP": "19138"} \N +37 3 \N 527791780 22 16517680 GACAA G 100 {22-16517680-GACAA-G} \N 0.000599041523 PASS 22-16517680-GACAA-G 3 5008 {"DP": "23980"} \N +38 3 \N 538489066 22 16539541 A AC 100 {22-16539541-A-AC} \N 0.00139776361 PASS 22-16539541-A-AC 7 5008 {"DP": "19363"} \N +39 3 \N 374006257 22 16577044 TG AG 100 {22-16577044-TG-AG,22-16577044-TG-T} \N 0.0033945688 PASS 22-16577044-TG-AG 17 5008 {"DP": "14269"} \N +40 3 \N 200929253 22 16577044 TG T 100 {22-16577044-TG-AG,22-16577044-TG-T} \N 0.00938498415 PASS 22-16577044-TG-T 47 5008 {"DP": "14269"} \N +41 3 \N 371560503 22 16879601 T TA 100 {22-16879601-T-TA,22-16879601-T-TAA} \N 0.062699683 PASS 22-16879601-T-TA 314 5008 {"DP": "18393"} \N +42 3 \N 371560503 22 16879601 T TAA 100 {22-16879601-T-TA,22-16879601-T-TAA} \N 0.0231629387 PASS 22-16879601-T-TAA 116 5008 {"DP": "18393"} \N +43 3 \N 5994030 22 17302972 C A 100 {22-17302972-C-A} \N 0.58526355 PASS 22-17302972-C-A 2931 5008 {"DP": "14904"} \N +44 3 \N 5748665 22 17300408 A G 100 {22-17300408-A-G} \N 0.943091035 PASS 22-17300408-A-G 4723 5008 {"DP": "17781"} \N +45 3 \N 5844283 22 17301526 ATACATAGTC A 100 {22-17301526-ATACATAGTC-A} \N 0.585463285 PASS 22-17301526-ATACATAGTC-A 2932 5008 {"DP": "5287"} \N +46 3 \N 553611103 22 19617927 GTCT GTCTTCT 100 {22-19617927-GTCT-GTCTTCT,22-19617927-GTCT-GTCTTCTTCT,22-19617927-GTCT-G} \N 0.023562301 PASS 22-19617927-GTCT-GTCTTCT 118 5008 {"DP": "24087"} \N +47 3 \N 553611103 22 19617927 GTCT GTCTTCTTCT 100 {22-19617927-GTCT-GTCTTCT,22-19617927-GTCT-GTCTTCTTCT,22-19617927-GTCT-G} \N 0.0033945688 PASS 22-19617927-GTCT-GTCTTCTTCT 17 5008 {"DP": "24087"} \N +48 3 \N 148427666 22 19617927 GTCT G 100 {22-19617927-GTCT-GTCTTCT,22-19617927-GTCT-GTCTTCTTCT,22-19617927-GTCT-G} \N 0.0363418534 PASS 22-19617927-GTCT-G 182 5008 {"DP": "24087"} \N +49 3 \N 374006257 2 16577044 TG AG 100 {2-16577044-TG-AG,2-16577044-TG-T} \N 0.0033945688 PASS 2-16577044-TG-AG 17 5008 {"DP": "14269"} \N +50 3 \N 200929253 2 16577044 TG T 100 {2-16577044-TG-AG,2-16577044-TG-T} \N 0.00938498415 PASS 2-16577044-TG-T 47 5008 {"DP": "14269"} \N +\. +COPY data.variant_genes (id, variant, gene) FROM stdin; +1 1 6 +2 2 6 +3 3 6 +4 4 6 +5 5 6 +6 6 6 +7 7 6 +8 8 6 +9 9 6 +10 10 6 +11 11 6 +12 12 6 +13 13 6 +14 14 6 +15 15 6 +16 16 6 +17 17 7 +18 18 7 +19 19 1 +20 20 2 +21 20 1 +22 21 1 +23 22 1 +24 23 1 +25 24 1 +26 25 1 +27 26 1 +28 28 1 +29 29 1 +30 30 4 +31 30 3 +32 31 4 +33 31 3 +34 32 5 +35 32 4 +36 33 8 +\. +COPY data.variant_transcripts (id, variant, transcript) FROM stdin; +1 1 11 +2 1 16 +3 1 7 +4 1 12 +5 1 15 +6 1 8 +7 1 13 +8 1 9 +9 1 14 +10 1 10 +11 2 11 +12 2 16 +13 2 7 +14 2 12 +15 2 15 +16 2 8 +17 2 17 +18 2 13 +19 2 9 +20 2 14 +21 2 10 +22 3 11 +23 3 16 +24 3 7 +25 3 12 +26 3 15 +27 3 8 +28 3 17 +29 3 13 +30 3 9 +31 3 14 +32 3 10 +33 4 11 +34 4 16 +35 4 7 +36 4 12 +37 4 15 +38 4 8 +39 4 17 +40 4 13 +41 4 9 +42 4 14 +43 4 10 +44 5 11 +45 5 16 +46 5 7 +47 5 12 +48 5 15 +49 5 8 +50 5 17 +51 5 13 +52 5 9 +53 5 14 +54 5 10 +55 6 11 +56 6 16 +57 6 7 +58 6 12 +59 6 15 +60 6 8 +61 6 17 +62 6 18 +63 6 13 +64 6 9 +65 6 14 +66 6 10 +67 7 11 +68 7 16 +69 7 19 +70 7 15 +71 7 8 +72 7 17 +73 7 18 +74 7 13 +75 7 9 +76 7 14 +77 7 10 +78 8 11 +79 8 16 +80 8 19 +81 8 15 +82 8 8 +83 8 17 +84 8 18 +85 8 13 +86 8 9 +87 8 14 +88 8 10 +89 9 11 +90 9 16 +91 9 20 +92 9 17 +93 9 18 +94 9 13 +95 9 9 +96 9 14 +97 9 10 +98 10 11 +99 10 16 +100 10 20 +101 10 17 +102 10 18 +103 10 13 +104 10 9 +105 10 14 +106 10 10 +107 11 11 +108 11 16 +109 11 20 +110 11 17 +111 11 18 +112 11 13 +113 11 9 +114 11 14 +115 11 10 +116 12 11 +117 12 16 +118 12 20 +119 12 17 +120 12 18 +121 12 13 +122 12 9 +123 12 14 +124 12 10 +125 13 11 +126 13 16 +127 13 20 +128 13 17 +129 13 18 +130 13 13 +131 13 9 +132 13 14 +133 13 10 +134 14 11 +135 14 16 +136 14 20 +137 14 17 +138 14 18 +139 14 13 +140 14 9 +141 14 14 +142 14 10 +143 15 11 +144 15 16 +145 15 20 +146 15 17 +147 15 18 +148 15 13 +149 15 9 +150 15 14 +151 15 10 +152 16 11 +153 16 16 +154 16 20 +155 16 17 +156 16 18 +157 16 13 +158 16 9 +159 16 14 +160 16 10 +161 17 23 +162 17 29 +163 17 24 +164 17 28 +165 17 21 +166 17 30 +167 17 27 +168 17 22 +169 17 25 +170 17 26 +171 18 23 +172 18 29 +173 18 24 +174 18 28 +175 18 21 +176 18 30 +177 18 27 +178 18 22 +179 18 26 +180 19 1 +181 19 2 +182 20 1 +183 20 2 +184 20 3 +185 21 1 +186 21 2 +187 22 1 +188 22 2 +189 23 1 +190 23 2 +191 24 1 +192 24 2 +193 25 1 +194 25 2 +195 26 1 +196 26 2 +197 28 1 +198 28 2 +199 29 1 +200 29 2 +201 30 5 +202 30 4 +203 31 5 +204 31 4 +205 32 6 +206 32 5 +207 33 31 +\. +COPY users.users (id, username, email, affiliation, country, identity, identity_type) FROM stdin; +\. +COPY users.dataset_access (id, dataset, user_id, wants_newsletter, is_admin) FROM stdin; +\. +COPY users.linkhash (id, dataset_version, user_id, hash, expires_on) FROM stdin; +\. +COPY users.sftp_users (id, user_id, user_uid, user_name, password_hash, account_expires) FROM stdin; +\. +COPY users.user_access_log (id, user_id, dataset, ts, action) FROM stdin; +\. +COPY users.user_consent_log (id, user_id, dataset_version, ts) FROM stdin; +\. +COPY users.user_download_log (id, user_id, dataset_file, ts) FROM stdin; +\. diff --git a/scripts/watch_frontend.py b/scripts/watch_frontend.py index 25bfff8c4..760dcaafb 100644 --- a/scripts/watch_frontend.py +++ b/scripts/watch_frontend.py @@ -1,9 +1,8 @@ -import inotify.adapters import re import subprocess import os import logging - +import inotify.adapters def files_to_watch(): r = re.compile("^/code/frontend/(templates|src)") @@ -18,7 +17,7 @@ def comb(*args): def install_node_deps(): os.chdir('frontend') - subprocess.call(['npm','install']) + subprocess.call(['npm', 'install']) os.chdir('..') def main(): @@ -31,12 +30,12 @@ def main(): grepper = comb(files_to_watch(), events_to_watch()) while True: - changes = list( filter(grepper, i.event_gen(timeout_s=0.5, yield_nones=False)) ) + changes = list(filter(grepper, i.event_gen(timeout_s=0.5, yield_nones=False))) if changes: logging.info("Files updated rerunning") for c in changes: (_, type_names, path, filename) = c - logging.info(" PATH=[{}] FILENAME=[{}] EVENT_TYPES={}".format(path, filename, type_names)) + logging.info(f" PATH=[{path}] FILENAME=[{filename}] EVENT_TYPES={type_names}") subprocess.call(['make']) diff --git a/settings_sample.json b/settings_sample.json index a530f12f0..11cfbe695 100644 --- a/settings_sample.json +++ b/settings_sample.json @@ -1,12 +1,6 @@ { "cookieSecret" : "Something random for tornado to sign cookies with", - "mysqlHost" : "127.0.0.1", - "mysqlPasswd" : "password", - "mysqlSchema" : "swefreq", - "mysqlUser" : "swefreq", - "mysqlPort" : 3306, - "postgresHost" : "postgres host", "postgresPort" : 5432, "postgresUser" : "postgres", diff --git a/sql/beacon_schema.sql b/sql/beacon_schema.sql index 4b3ed0a05..52d4908b9 100644 --- a/sql/beacon_schema.sql +++ b/sql/beacon_schema.sql @@ -103,7 +103,7 @@ CREATE OR REPLACE VIEW beacon.beacon_mate_table AS dm.allele_freq as frequency, dm.mate_start - 1 as "end", 'BND' as variantType - FROM data.mate AS dm + FROM data.mates AS dm JOIN beacon.available_datasets as av ON dm.dataset_version = av.id JOIN data.datasets as d diff --git a/sql/data_schema.sql b/sql/data_schema.sql index b7b2e9f0d..0d5de5b7e 100644 --- a/sql/data_schema.sql +++ b/sql/data_schema.sql @@ -173,7 +173,7 @@ CREATE TABLE IF NOT EXISTS data.variants ( ); -- For storing breakends -CREATE TABLE IF NOT EXISTS data.mate ( +CREATE TABLE IF NOT EXISTS data.mates ( id integer PRIMARY KEY GENERATED BY DEFAULT AS IDENTITY, dataset_version integer REFERENCES data.dataset_versions, chrom_id varchar(128), -- column 3 in vcf diff --git a/test/data/browser_test_data.sql b/test/data/browser_test_data.sql index c5966b1f6..aac3f713b 100644 --- a/test/data/browser_test_data.sql +++ b/test/data/browser_test_data.sql @@ -20,6 +20,7 @@ COPY data.studies (id, pi_name, pi_email, contact_name, contact_email, title, st COPY data.datasets (id, study, short_name, full_name, browser_uri, beacon_uri, beacon_description, avg_seq_depth, seq_type, seq_tech, seq_center, dataset_size) FROM stdin; 1 1 SweGen SweGen url \N \N 0 type method place 0 2 1 SweGen2 SweGen2 url \N \N 0 type method place 0 +3 1 Unrel Unreleased dataset url \N \N 0 type method place 0 \. COPY data.reference_sets (id, reference_build, reference_name, ensembl_version, gencode_version, dbnsfp_version) FROM stdin; @@ -32,6 +33,8 @@ COPY data.dataset_versions (id, dataset, reference_set, dataset_version, dataset 3 1 1 20171025 desc terms 2001-01-03 00:00:00 doi place email \N {1,5,10,15,20,25,30,50,100} TRUE REGISTERED PUBLIC 4 1 1 20180409 desc terms 2001-01-04 00:00:00 doi place email \N {1,5,10,15,20,25,30,50,100} TRUE REGISTERED PUBLIC 5 2 1 20190409 desc terms 2001-01-05 00:00:00 doi place email \N {1,5,10,15,20,25,30,50,100} TRUE REGISTERED PUBLIC +6 2 1 UNRELEASED desc terms 9999-12-31 00:00:00 doi place email \N {1,5,10,15,20,25,30,50,100} TRUE REGISTERED PUBLIC +7 3 1 UNRELEASED desc terms 9999-12-31 00:00:00 doi place email \N {1,5,10,15,20,25,30,50,100} TRUE REGISTERED PUBLIC \. COPY data.coverage (id, dataset_version, chrom, pos, mean, median, coverage) FROM stdin; diff --git a/test/travis_script.sh b/test/travis_script.sh index eae53190d..017a8f7ea 100755 --- a/test/travis_script.sh +++ b/test/travis_script.sh @@ -3,6 +3,7 @@ DBNAME=swefreq ## SETUP SETTINGS +echo '>>> Preparing for testing: Fix settings.json file' cp settings_sample.json settings.json sed -i.tmp 's/"postgresHost" : "postgres host"/"postgresHost" : "127.0.0.1"/' settings.json @@ -13,7 +14,8 @@ echo 'SETTINGS' cat settings.json echo '/SETTINGS' -echo '>>> Test 1. The SQL Patch' + +echo '>>> Test 1: The SQL Patch' LATEST_RELEASE=$(git tag | grep '^v' | sort -V | tail -n 1) git show "$LATEST_RELEASE:sql/*_schema.sql" > master-schema.sql @@ -23,21 +25,25 @@ psql -U postgres -h 127.0.0.1 -p 5433 -f sql/patch-master-db.sql "$DBNAME" # Empty the database psql -U postgres -h 127.0.0.1 -p 5433 "$DBNAME" <<__END__ -DROP SCHEMA data; -DROP SCHEMA users; +DROP SCHEMA data CASCADE; +DROP SCHEMA users CASCADE; __END__ -echo '>>> Test 2. Load the swefreq schema' + +echo '>>> Test 2: Load the swefreq schema' psql -U postgres -h 127.0.0.1 -p 5433 -f sql/data_schema.sql "$DBNAME" psql -U postgres -h 127.0.0.1 -p 5433 -f sql/user_schema.sql "$DBNAME" +psql -U postgres -h 127.0.0.1 -p 5433 -f sql/beacon_schema.sql "$DBNAME" psql -U postgres -h 127.0.0.1 -p 5433 -f test/data/load_dummy_data.sql "$DBNAME" psql -U postgres -h 127.0.0.1 -p 5433 -f test/data/browser_test_data.sql "$DBNAME" -echo '>>> Test 3. Check that the backend starts' + +echo '>>> Test 3: Check that the backend starts' (cd backend && ../test/01_daemon_starts.sh) -echo '>>> Test 4. the backend API' + +echo '>>> Test 4: The backend' COVERAGE_FILE=.coverage_server coverage run backend/route.py --port=4000 --develop 1>http_log.txt 2>&1 & BACKEND_PID=$! @@ -59,10 +65,14 @@ exit_handler () { trap exit_handler EXIT + +echo '>>> Test 4A: The backend API' RETURN_VALUE=0 python backend/test.py -v RETURN_VALUE=$((RETURN_VALUE + $?)) + +echo '>>> Test 4B: The browser backend' # test browser COVERAGE_FILE=.coverage_pytest PYTHONPATH=$PYTHONPATH:backend/ py.test backend/ --cov=backend/ RETURN_VALUE=$((RETURN_VALUE + $?)) @@ -71,7 +81,102 @@ RETURN_VALUE=$((RETURN_VALUE + $?)) curl localhost:4000/developer/quit sleep 2 # Lets wait a little bit so the server has stopped -coverage combine .coverage_pytest .coverage_server + +echo '>>> Prepare for test 5' +psql -U postgres -h 127.0.0.1 -p 5433 "$DBNAME" <<__END__ +DROP SCHEMA data CASCADE; +DROP SCHEMA users CASCADE; +__END__ + +psql -U postgres -h 127.0.0.1 -p 5433 -f sql/data_schema.sql "$DBNAME" +psql -U postgres -h 127.0.0.1 -p 5433 -f sql/user_schema.sql "$DBNAME" + +BASE=scripts/importer +ln -s tests/data "$BASE/downloaded_files" +gzip -c "$BASE/downloaded_files/dbNSFP_gene.txt" > "$BASE/downloaded_files/dbNSFP2.9_gene.gz" +gzip -c "$BASE/downloaded_files/gencode.gtf" > "$BASE/downloaded_files/gencode.v19.annotation.gtf.gz" +gzip "$BASE/tests/data/dataset1_1.vcf" +gzip "$BASE/tests/data/dataset1_1_coverage.txt" +gzip "$BASE/tests/data/dataset1_2.vcf" +gzip "$BASE/tests/data/dataset1_2_coverage.txt" +gzip "$BASE/tests/data/dataset2_1.vcf" + +echo '>>> Test 5. Importing data' + +sed -i -e 's/\"\$SCRIPT_DIR\/importer/COVERAGE_FILE=.coverage_import_1 coverage run \"\$SCRIPT_DIR\/importer/g' scripts/manage.sh +# read reference data +scripts/manage.sh import --add_reference\ + --gencode_version 19\ + --ensembl_version homo_sapiens_core_75_37\ + --assembly_id GRCh37p13\ + --dbnsfp_version 2.9.3\ + --batch_size 2\ + --ref_name GRCh37p13 + +# read dataset names, versions etc +psql -U postgres -h 127.0.0.1 -p 5433 -f "$BASE/tests/data/base_info.sql" "$DBNAME" + + +# read variant data +sed -i -e 's/import_1/import_2/' scripts/manage.sh +scripts/manage.sh import --add_raw_data \ + --dataset "Dataset 1"\ + --version "Version 1"\ + --variant_file "$BASE/tests/data/dataset1_1.vcf.gz"\ + --count_calls \ + --coverage_file "$BASE/tests/data/dataset1_1_coverage.txt.gz" + +sed -i -e 's/import_2/import_3/' scripts/manage.sh +scripts/manage.sh import --add_raw_data \ + --dataset "Dataset 1"\ + --version "Version 2"\ + --variant_file "$BASE/tests/data/dataset1_2.vcf.gz"\ + --batch_size 2\ + --coverage_file "$BASE/tests/data/dataset1_2_coverage.txt.gz" + +sed -i -e 's/import_3/import_4/' scripts/manage.sh +scripts/manage.sh import --add_raw_data \ + --dataset "Dataset 2"\ + --version "Version 1"\ + --count_calls \ + --variant_file "$BASE/tests/data/dataset2_1.vcf.gz"\ + --beacon-only + +# make pg_dump +# compare file to reference; must remove comments, empty rows and id column +pg_dump -U postgres -h 127.0.0.1 -p 5433 "$DBNAME" -f dbdump.psql --data-only +sed -i -r -e '/^--/d;/^$/d;s/^[0-9]+[^I]//' dbdump.psql +grep -v -P "^SE[TL]" dbdump.psql | sort > sdump.psql +sed -i -r -e 's/^[0-9]+[^I]//' "$BASE/tests/data/reference.psql" +sort "$BASE/tests/data/reference.psql" > ref.psql + +# compare dump to reference +diff sdump.psql ref.psql +RETURN_VALUE=$((RETURN_VALUE + $?)) + +echo '>>> Test 6. Reading manta file' + +sed -i -e 's/import_4/mate_1/' scripts/manage.sh +./scripts/manage.sh import --add_raw_data \ + --dataset "Dataset 1" \ + --version "Version 1" \ + --add_mates \ + --add_reversed_mates \ + --variant_file "$BASE/tests/data/manta.vcf" + +psql -U postgres -h 127.0.0.1 -p 5433 "$DBNAME" -c "select chrom_id, pos, ref, alt, chrom, mate_chrom, mate_start, mate_id, allele_freq, variant_id, allele_count, allele_num from data.mates ;" > mates_res.txt +diff mates_res.txt "$BASE/tests/data/mates_reference.txt" +RETURN_VALUE=$((RETURN_VALUE + $?)) + +echo '>>> Code evaluation' +pylint backend +RETURN_VALUE=$((RETURN_VALUE + $?)) +pylint scripts +RETURN_VALUE=$((RETURN_VALUE + $?)) + +echo '>>> Finalising: Combine coverage' + +coverage combine .coverage_pytest .coverage_server .coverage_import_1 .coverage_import_2 .coverage_import_3 .coverage_import_4 .coverage_mate_1 if [ -f .coverage ]; then coveralls