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Kurt-Hetrick / JHG_Clincal_Exome_Pipeline

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updating picard tools version for core exome pipeline #31

Open Kurt-Hetrick opened 2 years ago

Kurt-Hetrick commented 2 years ago

in particular for collecthsmetrics since it has higher coverage cap metrics available, but should consider upgrading for all processes/metrics that are obtained via picard tools. this could potentially be a sizable PITA, but now would be the time to do it as part of phase2. currently using 2.17. looking into at least 2.23.9. also looked at 2.26.2. generated collecthsmetrics using both versions and there was no difference b/w the two at least for the summary metrics. the mitochondrial worklow uses a version from gatk that is newer than 2.17, but less than 2.23.9. that version also does not have the higher coverage caps.

Kurt-Hetrick commented 1 year ago

note that the host operating system has too old of a kernel to use newer versions of picard