Eliminating panel mutations based on coverage of PoN
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16 months ago
vctrm67 ▴ 20

I have generated a callset of mutations, based on a gene panel, from GATK's Mutect using a panel of normals. However, I am trying to eliminate called mutations that don't lie within the coverage of the panel (comprised of WES samples) as the panel may not cover areas where there are reads in the gene panel. It seems to me that I would somehow need to get a combined interval set of coverage for the panel of normals, and then eliminate mutations that don't lie within one of those windows. Does anyone know how I would get such a interval set or know of a better way to do this?

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