GQ=0 but GT=0/0
GATK calls for SNP rs429358 don't look quite right in our project level vcf. This is one of the two SNPs that define the APOE e2,e3 and e4 (so just 3 haplotypes in region). About 1% of the 5000 samples have GQ=0 with a GT=0/0 and DP >30 . The nearby SNP rs7412 does not have this pattern (instead all GQ=99 for DP >30). . With a GQ=0, I was expecting a './.' instead. However,The 0/0 looks correct based on the IGV view of the bam in this region
Is this a bug or is something else going on?