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I am implementing a tool that uses reads to identify potential sites for cancer, but I need a reliable genotype call from non-cancerous tissue. Currently, I'm trying to use GATK to make those calls, filter out the bad, and then use the remaining calls when I look over the raw reads in the cancer tissue.
The problem I'm finding is that GATK doesn't provide a GQ for variants that are homozygous for the reference, and I don't know how to correlate the QUAL with the GQs from those homozygous non-ref. Is there a way that I'm overlooking to have GATK provide the GQ for homozygous reference non-variant sites?