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Mutect2 --mitochondria-mode .args file?

ajwilsajwils Baltimore, MD -- JH GenomicsMember
Relatively new to GATK and I'm looking to follow your double alignment strategy for the mutect 2 mitochondrial variant calling. I'm mainly working at the linux command line. Is there a usage example on how to setup the -I .args input file referenced in the GATK readme? Would it basically just be identical to the example input json file in the mito pipeline workflow?

Answers

  • ajwilsajwils Baltimore, MD -- JH GenomicsMember
    Or perhaps I'm misunderstanding the inputs. Does this need a .args file?

    Is there a command line usage example that would replicate the full wdl pipeline?
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