Update of AD field after SelectVariants

mbauermbauer Posts: 1Member
edited November 2012 in Ask the GATK team

Hi,

I used the UnifiedGenotyper (GATK 1.6) on a multi-sample set to call variants, and for some of the positions I get multiple mutated alleles. The genotype entries in the combined VCF file look like (GT:AD:DP:GQ:PL):

0/1:94,11,0:124:22.18:22,0,2485,209,2500,2709

0/2:27,0,54:81:99:1651,1726,2695,0,968,836

so it's three AD values per entry. Running SelectVariants yields the following line for the second example from above:

GT:AD:DP:GQ 0/1:27,0,54:81:99

Although it changed the genotype from 0/2 to 0/1, it did not update the AD field. I checked the forums, but I could not really find anything discussing specifically the update of AD, except for the GATK 2.2 release notes where it says SelectVariants: "Fixed bug where the AD field was not handled properly. We now strip the AD field out whenever the alleles change in the combined file."

I was wondering whether you could confirm if cases like the one above would benefit from the bugfix, or if the bug description applies to something else.

Thanks a lot for all your hard work,
Markus

Post edited by Geraldine_VdAuwera on

Answers

  • ebanksebanks Broad InstitutePosts: 687Member, Administrator, GATK Dev, Broadie, Moderator, DSDE Dev, GP Member admin

    Correct, this is the fix that was reported.

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

  • b0bb0b Posts: 1Member

    For a variant that has been stripped of the AD field, is there any way/tool avalibe that can re-populate this field? In the case of the AD field it is not clear to me why all values needed to be droped rather than just the value for the dropped allele. Cheers.

  • ebanksebanks Broad InstitutePosts: 687Member, Administrator, GATK Dev, Broadie, Moderator, DSDE Dev, GP Member admin

    No, this isn't possible currently. One should theoretically be able to use the Variant Annotator, but it's not hooked up appropriately with this particular annotation at the moment (but we're hoping to fix this at some point).

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

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