This is more of a feature request than anything else. I'm implementing the genotype refinement best practices guidelines for some trio WGS data sets. The probands are mostly male, and chrY causes CalculateGenotypePosteriors to choke. Is it possible to add a parameter which takes a list of intervals to skip processing? Using the exclude intervals parameter excludes chrY from the output entirely, which is not the behaviour I'm after. At the moment I'm pulling chrY out separately and then tacking it back in.
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