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Is there a best practice for finding compound heterozygotes using GATK? I can easily find recessive pattern variants using the SelectVariants tool, however, I have not been able to find a way to select compound hets. I am sure the Broad has a straightforward way. Is it somehow integrated into the GATK tool set?
I have considered using something like Gemini, but I would prefer to keep tools use to fewer product lines whenever possible.
Thanks for your help!