Excess values in VCF INFO/AD field

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7.7 years ago

oluwaseyi.shorinola ▴ 20

I have a multisample VCF4.2 file in which variants are called in two different samples against a reference genome. For variant site, the INFO fields DP;ADF;ADR;AD;AC1;DP4 . are returned as below:

CHROM POS ID REF ALT QUAL FILTER INFO
chr1A 100 . G C 30 . DP=5;ADF=1,1,0;ADR=0,3,0;AD=1,4,0;AC1=3;DP4=1,0,1,3

I am however getting 3 values in the ADF, ADR, and AD fields instead of two values i.e ref and alternate allele depth as expected for biallelic sites. And this is the same for all my ~20,000 biallelic sites. Can anyone kindly explain why this might be.

Many thanks

Olu

SNP • 2.6k views

ADD COMMENT • link 7.7 years ago by oluwaseyi.shorinola ▴ 20

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Splitting mulit-allelic sites into multiple vcf records will not clean up excess allele fields.

ADD REPLY • link 7.7 years ago by Zev.Kronenberg 12k

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did you discover why this happens? I have the same problem

ADD REPLY • link 7.1 years ago by dovi ▴ 60

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