Wrong genotype assignation in GATK?

Question

[Rob]

Hello,

I am looking at some GATK VCF results, and I found something I can't explain.

There is this result for one of my SNP:

GT:AB:AD:DP:GQ:MQ0:PL   0/1:1.00:21,0:22:79:0:79,0,708

The concerned field is the AD which is the "Allelic depths for the ref and alt alleles in the order listed".

How is it possible that the final genotype is 0/1 when the AD show no coverage for the alternative allele (AD=21,0)? Is this an error in GATK or am I misunderstanding something?

Thanks for your help,

Rob.

[Kevin Blighe]

I would take a look at the BAM file in IGV or some other viewer. All I know is that AD and DP don't actually report the same thing and that some level of filtering occurs in one. It's possible that the one filtered read that you observe contained the ref allele, which made the call heterozygous. Still an 'iffy' call, in that case, though.

A simple check in IGV should confirm.