Hello the team,
For some genotypes, it seems are wrong, I know it's model based, and base q, map q, etc are considered in the model. I also read this link: http://gatkforums.broadinstitute.org/discussion/1235/why-didnt-the-unified-genotyper-call-my-snp-i-can-see-it-right-there-in-igv#latest But my case are special, the format is (ref allele count)/(alternative allele count) genotype call: 22/24 0/0 109/125 0/0 85/109 0/0 26/32 0/0 40/161 0/0 195/6 1/1 239/5 1/1 83/6 1/1 46/28 1/1
In one case, the two variants are adjacent to each other. In some case, they are one base indels.