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docs: Update docs on file formats and fixing errors (#150)
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xiamaz authored Oct 6, 2023
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22 changes: 21 additions & 1 deletion docs/common_errors.rst
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Expand Up @@ -33,7 +33,7 @@ Explanation

Resolution
You can either submit a revision of your interpretation, (or, e.g., extend the "observed in" information), or leave it as is.
Revisions are coded by providing the ``clinvar_accession`` header in the TSV file.
Revisions are coded by providing the ``ACCESSION`` header in the TSV file.

----------------------------------
Submission Names Cannot be Changed
Expand All @@ -54,3 +54,23 @@ Resolution
Remove the old variant and add a new variant instead.
Note that ClinVar will store your "local variant ID".
If you resubmit a new record, make sure that this is changed or cleared such that ClinVar does not link your new request to your old submission and thinks you want to change your variant coordinates.

-----------------------------------------------------------
Multiple Conditions have been submitted without explanation
-----------------------------------------------------------

Message
You provided multiple diseases as the condition for the classification. If they
represent related diseases along a spectrum, provide ``uncertain`` for
multipleConditionExplanation. If they represent diseases that occur together in
an individual with the variant (this case is rare), provide ``co-occurring`` for
multipleConditionExplanation."

Explanation
Multiple Condition IDs have been submitted for single variant. Check if this
has been intentional. If multiple conditions are to be submitted, a reason
needs to be included with the submission.

Resolution
Explicitly add either ``Uncertain``, ``Co-occurring`` or ``Novel disease``
to the list of ``CONDITIONS``.
13 changes: 8 additions & 5 deletions docs/file_formats.rst
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Expand Up @@ -40,6 +40,9 @@ The following headers are optional:
- ``PMID`` - List of Pubmed IDs separated by a comma or semicolon, any space
will be stripped.
E.g., ``31859447‚29474920``.
- ``ACCESSION`` - Existing clinvar SCV for this variant. This should only be set
if the submitters organization has already uploaded the variant for the same
condition before.
- ``$remove_from_batch`` - you can use this for removing a previously added variant from the given batch; one of ``true`` and ``false``, defaults to ``false``.

Any further header will be imported into the local repository into an ``extra_data`` field.
Expand All @@ -49,8 +52,8 @@ The following shows an example.

.. code-block:: text
ASSEMBLY CHROM POS REF ALT OMIM MOI CLIN_SIG HPO
GRCh37 19 48183936 C CA 619325 Autosomal dominant inheritance Likely pathogenic HP:0004322;HP:0001263
ASSEMBLY CHROM POS REF ALT CONDITION MOI CLIN_SIG HPO
GRCh37 19 48183936 C CA OMIM:619325 Autosomal dominant inheritance Likely pathogenic HP:0004322;HP:0001263
Note that you cannot submission TSV imports with batches that contain removals already.

Expand All @@ -68,7 +71,7 @@ Clinvar-this will recognize the TSV file format based on these headers.
- ``SV_TYPE`` - the type of the structural variant; one of ``Insertion``, ``Deletion``, ``Duplication``, ``Tandem duplication``, ``copy number loss``, ``copy number gain``, ``Inversion``, ``Translocation``, ``Complex``.
Note that ClinVar does not allow you to specify the second end of a non-linear event (e.g., a fusion with another chromosome).
We suggest that you submit a second SV entry with the coordinate and link the two events in ``CLIN_COMMENT``.
- ``CONDITION`` - the OMIM id of the carrier's condition (not the OMIM gene ID), e.g., ``619325``, alternatively also MONDO, ORPHA and HPO-Terms are supported, if multiple conditions are given, a multiple condition qualifier (``Co-occurring``, ``Uncertain``, ``Novel disease``) should also be given as an additional term.
- ``CONDITION`` - the OMIM id of the carrier's condition (not the OMIM gene ID), e.g., ``OMIM:619325``, alternatively also MONDO, ORPHA and HPO-Terms are supported, if multiple conditions are given, a multiple condition qualifier (``Co-occurring``, ``Uncertain``, ``Novel disease``) should also be given as an additional term.
- ``MOI`` - mode of inheritance, e.g., ``Autosomal dominant inheritance`` or ``Autosomal recessive inheritance``
- ``CLIN_SIG`` - clinical significance, e.g. ``Pathogenic``, or ``Likely benign``

Expand All @@ -82,7 +85,7 @@ You have to provide all of them and cannot provide them together with ``START``

The following headers are optional:

- ``clinvar_accession`` - ClinVar SCV accession if any exists yet.
- ``ACCESSION`` - ClinVar SCV accession if any exists yet.
When this is set then this variant will be updated in the batch rather than added as a novel variant.
- ``CLIN_EVAL`` - date of late clinical evaluation, e.g. ``2022-12-02``, leave empty to fill with the date of today
- ``CLIN_COMMENT`` - a comment on the clinical significance, e.g., ``ACMG Class IV; PS3, PM2_sup, PP4``
Expand All @@ -102,7 +105,7 @@ The following shows an example.

.. code-block:: text
ASSEMBLY CHROM START STOP SV_TYPE OMIM MOI CLIN_SIG HPO
ASSEMBLY CHROM START STOP SV_TYPE CONDITION MOI CLIN_SIG HPO
GRCh38 chr1 844347 4398122 Deletion not provided Autosomal dominant inheritance HP:0001263
Note that you cannot submission TSV imports with batches that contain removals already.
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37 changes: 23 additions & 14 deletions docs/getting_started.rst
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Expand Up @@ -73,30 +73,39 @@ Check that this worked:
Prepare a clinvar-this TSV file
-------------------------------

You will need the following header in the first line

- ``ASSEMBLY`` - the assembly used, e.g., ``GRCh37``, ``hg19``, ``GRCh38``, ``hg38``
- ``CHROM`` - the chromosomal position without ``chr`` prefix, e.g., ``1``
- ``POS`` - the 1-based position of the first base in ``REF`` column
- ``REF`` - the reference allele of your variant
- ``ALT`` - the alternative allele of your variant
- ``OMIM`` - the OMIM id of the carrier's condition (not the OMIM gene ID), e.g., ``619325``.
Leave empty or use ``not provided`` if you have no OMIM ID.
- ``MOI`` - mode of inheritance, e.g., ``Autosomal dominant inheritance`` or ``Autosomal recessive inheritance``
- ``CLIN_SIG`` - clinical significance, e.g. ``Pathogenic``, or ``Likely benign``
You will need the following header in the first line. Mandatory columns have
been marked with a (*). See :doc:`file_formats` for further format details and instructions for
structural variants.

- ``ASSEMBLY`` * - the assembly used, e.g., ``GRCh37``, ``hg19``, ``GRCh38``, ``hg38``
- ``CHROM`` * - the chromosomal position without ``chr`` prefix, e.g., ``1``
- ``POS`` * - the 1-based position of the first base in ``REF`` column
- ``REF`` * - the reference allele of your variant
- ``ALT`` * - the alternative allele of your variant
- ``CONDITION`` * - ids for the carrier's condition, currently OMIM, ORPHA, MONDO
ids are supported, give these as ``OMIM|ORPHA|MONDO:123456``, e.g.
``OMIM:123456`` is a valid id, ``ORPHA12345`` is not. Can be left empty or use
``not provided`` if no condition should be published.
- ``MOI`` * - mode of inheritance, e.g., ``Autosomal dominant inheritance`` or ``Autosomal recessive inheritance``
- ``CLIN_SIG`` * - clinical significance, e.g. ``Pathogenic``, or ``Likely benign``
- ``CLIN_EVAL`` - optional, date of late clinical evaluation, e.g. ``2022-12-02``, leave empty to fill with the date of today
- ``CLIN_COMMENT`` - optional, a comment on the clinical significance, e.g., ``ACMG Class IV; PS3, PM2_sup, PP4``
- ``KEY`` - optional, a local key to identify the variant/condition pair.
Filled automatically with a UUID if missing, recommeded to leave empty.
Filled automatically with a UUID if missing, recommended to leave empty.
- ``HPO`` - List of HPO terms separated by comma or semicolon, any space will be stripped.
E.g., ``HP:0004322; HP:0001263``.
- ``PMID`` - List of literature references, give these as multiple numbers
separated by either ``,`` or ``;``. These will be listed as literature
references for the variant interpretation.
- ``ACCESSION`` - Give an SCV-identifier, if this variant has already been
previously uploaded by this institution and should be updated.

The following shows an example.

.. code-block:: text
ASSEMBLY CHROM POS REF ALT OMIM MOI CLIN_SIG HPO
GRCh37 19 48183936 C CA 619325 Autosomal dominant inheritance Likely pathogenic HP:0004322;HP:0001263
ASSEMBLY CHROM POS REF ALT CONDITION MOI CLIN_SIG HPO
GRCh37 19 48183936 C CA OMIM:619325 Autosomal dominant inheritance Likely pathogenic HP:0004322;HP:0001263
Note that you must use TAB characters (``\t``) for separating the file.

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