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

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