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Does Mutect2 have a multiple-thread setting?

Hi there,
I am running Mutect2 on my computer cluster? The walltime setting for my cluster is 200 hours. The data is relatively large. Mutect2 is running too slow, even exceed 200 hours...I was wondering if Mutect2 can use multiple threads.

Best Answer

  • bhanuGandhambhanuGandham Cambridge MA admin
    Accepted Answer

    HI @lei_yu

    No we do not support multi threading with mutect2. Are you using the latest GATK4.1.1.0 version? if not I recommend you do. There have been significant speed improvements with the latest version.


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