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How to filter VCF where at least x% of the individuals have DP>=10 and GQ>=20

Hi,

I would like filter the vcf file using DP and GQ thresholds at sites where atleast 80% of the individuals meeting the thresholds. More precisely, i have the below two scenarios:

  1. Retain sites where atleast 80% of the individuals had at least depth DP >= 10 and GQ>=20 irrespective of the reference or non-reference allele.

  2. Retain sites where atleast one sample has the non-reference allele with DP>= 10 and GQ >= 20.

I checked the vcftools documentation but could not find where i could specify the minimum number of individuals. I believe there could an existing thread or solution to acheive this. Could someone refer the solution here.

vcf filter gatk
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updated by Pierre Lindenbaum Pierre Lindenbaum • written by hellbio hellbio

1 answer

using vcffilterjdk : http://lindenb.github.io/jvarkit/VcfFilterJdk.html

Retain sites where atleast 80% of the individuals had at least depth DP >= 10 and GQ>=20 irrespective of the reference or non-reference allele

 java -jar dist/vcffilterjdk.jar -e 'return variant.getGenotypes().stream().filter(G->G.getDP()>=10 && G.getGQ()>=20).count()/(double)variant.getNSamples() > 0.8;' input.vcf

Retain sites where atleast one sample has the non-reference allele with DP>= 10 and GQ >= 20.

$ java -jar dist/vcffilterjdk.jar -e 'return variant.getGenotypes().stream().anyMatch(G->G.getDP()>=10 && G.getGQ()>=20 && G.getAlleles().stream().anyMatch(A->A.isCalled() && !A.isReference())) ;'
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written by Pierre Lindenbaum Pierre Lindenbaum

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