Placeholder for XHMM documentation article

Geraldine_VdAuweraGeraldine_VdAuwera Posts: 8,043Administrator, GATK Dev admin

XHMM documentation articles coming soon.

Geraldine Van der Auwera, PhD

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Comments

  • santinosantino Posts: 20Member

    Hi, is it possible to integrate the XHMM into GATK so that people can use Queue to run it? Thanks a lot!

  • fromerfromer NYCPosts: 20Member, Third-party Developer, GSA Collaborator

    Hi,

    There is indeed a Qscript to run XHMM currently distributed in:
    public/scala/qscript/org/broadinstitute/sting/queue/qscripts/CNV/xhmmCNVpipeline.scala

    We have yet to provide documentation, so you;d have to familiarize yourself with running Queue scripts more generally before you attempt this yet:
    http://gatkforums.broadinstitute.org/discussion/1306/overview-of-queue

    We hope to document this XHMM script more thoroughly in the coming months.

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