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Parallelizing GATK4 tools

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
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written by vctrm67 • vctrm67

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

https://xkcd.com/285/

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written by Pierre Lindenbaum Pierre Lindenbaum

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

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written by Kevin Blighe Kevin Blighe

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

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written by vctrm67 • vctrm67

Got a link? The question was just ignored?

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written by Kevin Blighe Kevin Blighe

I see. So, they will get back to you when they have time.

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written by Kevin Blighe Kevin Blighe

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