FilterMutectCalls: Missing documentation for --mitochondria-mode

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Alexander Koc

• January 19, 2024 15:05

Hi,

Hope this is the correct place to post this: The documentation for the FilterMutectCalls --mitochondria-mode flag is missing info about what the mode actually does.

See here for example: https://gatk.broadinstitute.org/hc/en-us/articles/13832694001563-FilterMutectCalls#--mitochondria-mode

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  Can Kockan

  • January 25, 2024 16:13
  • Edited

  Looks like it is missing the information indeed, and also for microbial mode. While waiting for a fix, here's the actual documentation, from: https://github.com/broadinstitute/gatk/blob/e796d20a9e0c0d311db56beeb58cae9ff03bb6d7/src/main/java/org/broadinstitute/hellbender/tools/walkers/mutect/filtering/M2FiltersArgumentCollection.java#L40

  Mitochondria mode excludes the filters ClusteredEventsFilter, MultiallelicFilter, PolymeraseSlippageFilter, FilteredHaplotypeFilter, FragmentLengthFilter, and GermlineFilter

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  Alexander Koc

  • January 26, 2024 07:59

  Thank you!

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