VCF format: what does AD 1,0 denote?

Question

[jtwalker]

I'm looking at one of my VCF files and I noticed that allele depth (AD) isn't just one number, but rather two values seperated by a comma

e.g.: GT:AD:DP:GQ:PL 0/0:1,0:1:3:0,3,27

The GATK doc doesn't really seem all that helpful here, as it doesn't explicitly describe what the two numbers are used for.

Can anyone explain? Thanks!

Answer 1

[Pierre Lindenbaum]

the definition of the attribute is defined in the header

 grep '=AD,'  test_vcf01.vcf
##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">

see also the VCF spec https://samtools.github.io/hts-specs/VCFv4.2.pdf

GT:AD:DP:GQ:PL 0/0:1,0:1:3:0,3,27

so we have a number for each allele (REF and all ALT alleles). Here one short read carries the REF allele and none carry the ALT. DP (depth) is 1 (1+0==1)