Extracting FILTER field from gnomAD vcf file
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Entering edit mode
5 months ago

Dear all,

My goal is to use PyVCF to process variants taken for GRCh37 and gnomAD v2.

On the gnomAD vcf file there is the filter field containing the following information:

##FILTER=<ID=AC0,Description="Allele count is zero after filtering out low-confidence genotypes (GQ < 20; DP < 10; and AB < 0.2 for het calls)">
##FILTER=<ID=InbreedingCoeff,Description="InbreedingCoeff < -0.3">
##FILTER=<ID=PASS,Description="Passed all variant filters">
##FILTER=<ID=RF,Description="Failed random forest filtering thresholds of 0.055272738028512555, 0.20641025579497013 (probabilities of being a true positive variant) for SNPs, indels">

Using PyVCF works fine for all other fields (pos, ref, alt and info). However for the filter field, for most of the variants I get the empty list:

print(variant.FILTER)
# will print: []

For a scarce amount of variants I get ['AC0', 'RF'] or ['ACO'].

Does the empty list mean that the FILTER is PASS as shown in the function: _parse_filter() in the parser code?

My installed PyVCF version is 0.6.8.

Thank you and keep safe!

vcf PyVCF gnomAD • 241 views
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Entering edit mode
5 months ago
Ram 32k

From the code, it does look like if PASS return [] will give you an empty array if the site is a PASS.

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Entering edit mode

Thank you very much! I will mark it as resolved for now.

Keep safe :)

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