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Many reference reads found with GQ=0 and cannot be visualized

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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?

Many thanks,

Xin


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