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How to emit only "Keep" or "Covered" calls from MuTect

nroaknroak HoustonMember ✭✭
edited September 2015 in MuTect v1

I'm interested in running muTect in a way that it emits only the Pass/Keep calls and filters out all the "Reject" calls internally.
I spent a lot of time on this forum but couldn't find any definite option or flag for this. I understand that I could simply do
'grep -v "REJECT"'
But I was looking to generate an output file that would be passed to next queue command directly.



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