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Kurt-Hetrick / CIDR_SOMATIC_WES_PIPELINES

currently for paired tumor - normal WES samples processed with TWIST UMIs
MIT License
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CollectVariantCallingMetrics bed files. 1 or 0 based. #38

Open Kurt-Hetrick opened 1 year ago

Kurt-Hetrick commented 1 year ago

I don't know! I made them 1-based for devivo so I would like to think that there was a reason that I did so, but I'll have to double check and make sure now.

Kurt-Hetrick commented 9 months ago

to clarify for my sanity. this was NOT for mutect2. this was for CollectVariantCallingMetrics called from gatk. I typically called this from picard tools in the past, but for various reasons I called this from gatk instead. based on the fact that it required a picard style interval file which is one based, i would assume that this is a direct port over from picard tools, but I should triple check to be sure. also changing title of issue so I don't freak out every time i see it. this also means that I'm not as concerned about an off by one error as it won't affect the metrics all that much even if it is wrong, but i should make it right regardless