During a manual review of a clinically important gene in a WGS sample, we noticed several SVs and a drop in coverage spanning at least two exons. The deletion doesn't look like a complete loss of an allele might be a mosaic gCNV. Testing with the GATK gCNVs didn't pick it up, and also it didn't work with the parameters to increase the sensitivity.
My question: There is a drop in the denoised ploidies in these regions (~1.5). But, I couldn't find a parameter or option that I could make use of this information. Changing a parameter to accommodate this might increase false-positive calls, but I would like to try it. Are there any options I could use here?
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