Question: Extracting FILTER field from gnomAD vcf file
0
gravatar for Damianos P. Melidis
10 weeks ago by
Germany/Hannover/Leibniz University Hannover
Damianos P. Melidis30 wrote:

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!

gnomad pyvcf vcf • 155 views
ADD COMMENTlink written 10 weeks ago by Damianos P. Melidis30
2
gravatar for _r_am
9 weeks ago by
_r_am32k
Baylor College of Medicine, Houston, TX
_r_am32k wrote:

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

ADD COMMENTlink written 9 weeks ago by _r_am32k

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

Keep safe :)

ADD REPLYlink written 9 weeks ago by Damianos P. Melidis30
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