AD and DP in VCF from ReduceRead BAMs

MonkolMonkol BostonMember, Broadie, Dev Posts: 14
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 Administrator, Dev Posts: 153 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 Administrator, Dev Posts: 153 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 InstituteMember, Administrator, Broadie, Moderator, Dev Posts: 698 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 -- Director, Data Sciences and Data Engineering, Broad Institute of Harvard and MIT

Answers

  • Mark_DePristoMark_DePristo Administrator, Dev Posts: 153 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 BostonMember, Broadie, Dev Posts: 14

    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 Administrator, Dev Posts: 153 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 InstituteMember, Administrator, Broadie, Moderator, Dev Posts: 698 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 -- Director, Data Sciences and Data Engineering, Broad Institute of Harvard and MIT

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