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:
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,