Many reference reads found with GQ=0 and cannot be visualized
Dear GATK Team,
I've seen a phenomenon that I've been struggling to explain:
Using HaplotypeCaller, at one particular locus, there seems to be 192 reference reads, however, the GQ is zero, with the output GT:DP:GQ:MIN_DP:PL 0/0:192:0:192:0,0,0
I used the -ERC GVCF flag to get reference coverage as well. I also tried the --emitDroppedReads with the -bamout flags to get any reads that aligned to this region, but still couldn't see anything from IGV.
Would you have any insight into the cause of this GQ=0 with so many reads?