GATK assigns a GT in contrast to AD
Posted in Ask the GATK team | Last updated on


Comments (4)

Dear Team, I was looking at a VCF file produced with UnifiedGenotyper (2.4.9). It is a multisample call and, for a limited number of calls, I have genotypes that are telling the exact opposite of AD field, as in this case

GT:AD:DP:GQ:PL  1/1:10,1:11:3:24,3,0

or

GT:AD:DP:GQ:PL  1/1:18,1:19:3:22,3,0

I have ten reads supporting the reference allele, 1 read supporting the alternate and the genotype is 1/1. This is happening in ~200 sites per sample in my dataset. I've checked the other way around and I found <100 sites in which the genotype is called 0/0 and theĀ AD suggests 1/1 or (more frequently) 0/1. This seems to happen in sites in which the number of variant samples is low (no more than 3 samples in a set of ~50 samples) and it is puzzling me a lot. Can you give me a comment on why this is happening? Thanks

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