Vcf export #241
Vcf export #241
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…ters_sanity_check_expr to vcf.py from gnomad_qc. Also added INFO_DICT, FORMAT_DICT, and make_vcf_filter_dict from ukb repo
…_dict to update INFO_DICT with AS fields and their values
…IELDS, REGION_TYPE_FIELDS, ALLELE_TYPE_FIELDS
gnomad/utils/vcf.py
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| return header_hist_dict | ||
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| def sample_sum_check( |
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This is something we want to check on the internal HT sanity checks right? I think it should also be moved somewhere else like the other function I mentioned above, but again not positive where to put it
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Agreed, this could go into an assessment/sanity_checks.py type file
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Yeah, I think this should move to keep this script VCF focused and assessment/sanity_checks.py sounds good to me for this and the one above it
…ts/their descriptions
gnomad/utils/vcf.py
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| if faf: | ||
| female_metrics.extend([x for x in female_metrics if "faf" in x]) |
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I'm confused by this line: it looks like you're extending the existing list female_metrics by faf elements that are already in the list
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faf elements aren't in the list -- female_metrics first pulls all annotations that contain _female and then corrects that list to keep only elements with both _female and AC, AN, or nhomalt. the faf annotations (faf95_female) don't contain AC, AN, or nhomalt, so they aren't kept in that step.
that said, why do we set AC, AN, and nhomalt to 0 but leave AF? I'm going to change this to just be female_metrics = [x for x in metrics if "_female" in x] if that works with you and @jkgoodrich
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hmm, interesting that AF is not set to 0. I will defer to @gtiao for this one, there may have been motivation for this that I am not aware of.
…ts/their descriptions
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A few more smaller changes requested, but it's looking really good. Thank you @ch-kr!
gnomad/utils/vcf.py
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| return header_hist_dict | ||
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| def sample_sum_check( |
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Yeah, I think this should move to keep this script VCF focused and assessment/sanity_checks.py sounds good to me for this and the one above it
gnomad/utils/vcf.py
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| ht_orig.select(*display_fields).show() | ||
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| def make_filters_sanity_check_expr(ht: hl.Table) -> Dict[str, hl.expr.Expression]: |
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agree, let's make an assessment/sanity_checks.py
gnomad/utils/vcf.py
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| if faf: | ||
| female_metrics.extend([x for x in female_metrics if "faf" in x]) |
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hmm, interesting that AF is not set to 0. I will defer to @gtiao for this one, there may have been motivation for this that I am not aware of.
…heck, make_filters_sanity_check_expr to assessment
| combos = make_label_combos(label_groups) | ||
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| for combo in combos: | ||
| combo_fields = combo.split("_") | ||
| group_dict = dict(zip(group_types, combo_fields)) | ||
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| for_combo = make_combo_header_text("for", group_dict, prefix) |
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Great idea for streamlining the code a bit!
| f"{prefix}hom": "|".join( | ||
| map(lambda x: f"{x:.1f}", ht.head(1).age_hist_hom.collect()[0].bin_edges) | ||
| ), | ||
| f"{prefix}{call_type}": "|".join( |
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Another nice consolidation of code
| Displays the number of rows in the Table that match the `cond_expr` and fail to be the desired condition (`check_description`). | ||
| If the number of rows that match the `cond_expr` is 0, then the Table passes that check; otherwise, it fails. | ||
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| .. note:: |
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Thank you for adding this note -- it's probably something easily missed when setting up the generic field check, so it's great to have this additional reminder
Added constants and some functions that are used during MT/HT>VCF export