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Disable duplicate read filter for M2

FPBarthelFPBarthel HoustonMember ✭✭

I have high coverage targeted sequencing data and would like to disable the duplicate read filter for Mutect2 (rather than skipping the de-duplication step in alignment).

Do I understand the documentation correctly that I should add the parameter --disable-read-filter NotDuplicateReadFilter to the Mutect2 call? I would do this both for the tumor-only M2 (PON step) and paired M2 (calling step).


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