AD and DP in VCF from ReduceRead BAMs

MonkolMonkol Posts: 6Member
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?
Thanks.

Post edited by Geraldine_VdAuwera on
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Best Answers

  • Mark_DePristoMark_DePristo Posts: 153Administrator, GATK Dev admin
    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 A. DePristo, Ph.D.
    Co-Director, Medical and Population Genetics
    Broad Institute of MIT and Harvard

  • Mark_DePristoMark_DePristo Posts: 153Administrator, GATK Dev admin
    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.

    --
    Mark A. DePristo, Ph.D.
    Co-Director, Medical and Population Genetics
    Broad Institute of MIT and Harvard

  • ebanksebanks Broad InstitutePosts: 689Member, Administrator, GATK Dev, Broadie, Moderator, DSDE Dev, GP Member admin
    Answer ✓

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

    Eric Banks, PhD -- Senior Group Leader, MPG Analysis, Broad Institute of Harvard and MIT

Answers

  • Mark_DePristoMark_DePristo Posts: 153Administrator, GATK Dev admin
    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 A. DePristo, Ph.D.
    Co-Director, Medical and Population Genetics
    Broad Institute of MIT and Harvard

  • MonkolMonkol Posts: 6Member

    Thanks Mark!
    But it should be okay for SNPs?
    Also does ReduceRead cause the AD to be summarized to 1,0 or 0,1 for homozygotes?

  • Mark_DePristoMark_DePristo Posts: 153Administrator, GATK Dev admin
    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.

    --
    Mark A. DePristo, Ph.D.
    Co-Director, Medical and Population Genetics
    Broad Institute of MIT and Harvard

  • ebanksebanks Broad InstitutePosts: 689Member, Administrator, GATK Dev, Broadie, Moderator, DSDE Dev, GP Member admin
    Answer ✓

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

    Eric Banks, PhD -- Senior Group Leader, MPG Analysis, Broad Institute of Harvard and MIT

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