Parallelizing GATK4 tools

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5.0 years ago

vctrm67 ▴ 90

Is there a way to parallelize GATK 4.1.2.0 tools (specifically Mutect2 and HaplotypeCaller? I had saw that GATK transitioned to Spark but I also read that people had issues using it and it didn't work perfectly...

Edit: https://github.com/broadinstitute/gatk/issues/5717

HaplotypeCallerSpark How to use

Pararellization in GATK 4

GATK • 1.7k views

ADD COMMENT • link 5.0 years ago by vctrm67 ▴ 90

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I also read that people had issues using it and it didn't work perfectly...

ADD REPLY • link 5.0 years ago by Pierre Lindenbaum 166k

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Edited original post.

ADD REPLY • link 5.0 years ago by vctrm67 ▴ 90

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Hi, I think that you should post this at the GATK Support Forum.

ADD REPLY • link 5.0 years ago by Kevin Blighe 89k

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I have, but they are not answering these types of questions right now.

ADD REPLY • link 5.0 years ago by vctrm67 ▴ 90

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Got a link? The question was just ignored?

ADD REPLY • link 5.0 years ago by Kevin Blighe 89k

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https://gatk.broadinstitute.org/hc/en-us/community/posts/360062233271-Parallelizing-Mutect2