Pipelining all the GATK steps with Queue

rcholicrcholic DenverMember

I've read the documentation on running GATK with Queue, but I did not find an answer to my question: how to write a QScript that allows Queue to run GATK from the Bam files (prepared by PiCard) all the way down to VCF files output. I want to minimize the intermediate files as much as possible. Is there any examples that you can point me to?

Answers

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Have you looked at the example qscripts in the github repo?

    Otherwise we will have a bunch more docs available by the end of the week; we're doing a big push right now to beef up our Queue docs ahead of the upcoming Queue workshop.

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