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