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We’re moving the GATK website, docs and forum to a new platform. Read the full story and breakdown of key changes on this blog.
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Test-drive the GATK tools and Best Practices pipelines on Terra


Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.

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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