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AD and DP in VCF from ReduceRead BAMs

MonkolMonkol BostonMember, Broadie
edited October 2012 in Ask the GATK team

Does the relationship between AD and DP stil hold in VCF produced from ReduceRead BAMs?
That is the sum of AD is <= DP
Or can other scenarios now occur?

Also is AD summarized to 1,0 or 0,1 for homozygous REF and ALT?


Best Answers

  • Mark_DePristoMark_DePristo Broad Institute admin
    Accepted Answer

    Unfortunately I literally -- like 2 minutes ago -- fixed a bug where the DP for indels wasn't being calculated correctly. Going forward the AD <= DP should hold for reduced reads but if you are looking at indels right now I'd take DP ~= sum(AD)

  • Mark_DePristoMark_DePristo Broad Institute admin
    Accepted Answer

    Everything should be fine for snps. And no, it's full read depth counts, so you see lines like 50,0:55 for AD and DP even from reduced reads output.

  • ebanksebanks Broad Institute ✭✭✭✭
    Accepted Answer

    No, Monkol is correct. My fixes for annotations (DP, AD, and FS) won't make it public until the upcoming 2.2 release.


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