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How can I run ComputeReadDepthCoverage separately to get only depth.dat output file

How can I run ComputeReadDepthCoverage separately to get only depth.dat output file

Answers

  • bhandsakerbhandsaker Member, Broadie ✭✭✭✭

    If you just want to run on a single bam file, ComputeReadDepthCoverage is a standard GATK walker so you can invoke it like any other walker. See the documentation for arguments (or alternatively do a dry run with the SVPreprocess.q script and see what is passed).

    gatkforums.broadinstitute.org/discussion/1495/computereaddepthcoverage

    Which leads to the second possible answer: You can edit the SVPreprocess.q script to create a custom script that only runs the phases up to and including ComputeReadDepthCoverage. Newer versions in the interim releases allow filtering based on the insert size distributions and so require the insert size distributions to be computed first.

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