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When I force GATK to call SNPs that are homozygous for the reference, it fails to provide a GQ. I realize that the GQ is dependent on an estimation of the frequency of the alternate, which doesn't make too much sense for monomorphic sites, but we want to use GQ as a filter for valid calls, since GQ and QUAL are so different.
Version 1.0 of GATK did provide this information, but apparently that changed as they fixed some bugs.
Does anyone know of a trick to get GATK to produce the GQ for those sites? If not, what do folks who need to know that a homozygous for reference call is valid (such as when you are comparing blood calls with tumor base counts).
Version 1.0 of GATK did provide this information, but apparently that changed as they fixed some bugs.
Does anyone know of a trick to get GATK to produce the GQ for those sites? If not, what do folks who need to know that a homozygous for reference call is valid (such as when you are comparing blood calls with tumor base counts).