DepthOfCoverage

SystemSystem Posts: 226Administrator admin
edited April 2013 in Tool Bulletin

A new tool has been released!

Check out the documentation at DepthOfCoverage.

Post edited by Geraldine_VdAuwera on

Comments

  • allinavallinav Posts: 4Member

    @Geraldine_VdAuwera, thank you for your tireless maintenance of the GATK forums and documentation. Could I ask for some clarification on the DepthOfCoverage tool bulletin and its docs?

    If I'm not mistaken, this posting was made for the DepthOfCoverage tool/walker? But the URL points to the VariantAnnotator annotation.

    Here is the tool documentation link:

    broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_coverage_DepthOfCoverage.html

    Second, in the tool documentation itself: the command line example calls the walker as "-T Coverage" but GATK says no such walker exists. That should be "-T DepthOfCoverage", yes?

    Thanks again!

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 8,023Administrator, GATK Dev admin

    Ah, yes, there was a mixup because at the time we had an annotator and the tool itself that had the same name, so the automated system that builds the tech docs got confused. Thanks for pointing this out, I'll correct the link here.

    And you are correct that the tool command line example should say -T DepthOfCoverage. That must have been a side-effect of when we renamed the annotator module to just "Coverage" to disambiguate the two. I will correct that as well.

    Good catches!

    Geraldine Van der Auwera, PhD

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