why new version mutect2 output vcf add DP?

manbamanba Member ✭✭
edited January 5 in Ask the GATK team

I find the result of mutect2 in gatk4.0.11.0 differs from 4.0.0.0 in vcf structure.
GT:AD:AF:DP:F1R2:F2R1(4.0.11.0)
GT:AD:AF:F1R2:F2R1(4.0.0.0)
why this need a change? and for example in new version
GT:AD:AF:DP: the value is 0/1:31,34:0.522:65:
but I once read something in somatic vcf, the first value of AD does not stands for ref reads, is it true, thanks a lot.

and can you tell me AF is usually smaller or bigger then the value in AD(I mean first /(first + second), here 34/(31+34))

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

FORMAT=<ID=AF,Number=A,Type=Float,Description="Allele fractions of alternate alleles in the tumor">

FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">

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