Incorrect missing genotypes using HaplotypeCaller
Dear GATK community,
I am using HaplotypeCaller for variant discovery and I have found some strange results in my VCF.
It appears that this walker is making no calls in positions with reads of support for them in the original BAM.
For instance this position:
chr7 302528 rs28436118 A G 31807.9 PASS . GT:AD:DP:GQ:PL 1/1:0,256:256:99:8228,767,0 ./.:98,0:98:.:. ./.:81,0:81:.:. 1/1:0,134:134:99:4287,401,0
was not called for 2 of the 4 samples available. However, in both samples where the genotype is missing there are many reads supporting an homozygous reference call (0/0).
Do you have any idea of why this is happening?