multithreading for MUTECT1

BogdanBogdan Palo Alto, CAMember ✭✭

Dear all, I was reading about the multithreading for GATK (https://www.broadinstitute.org/gatk/guide/article?id=1988), and I was wondering: will MUTECt1 also support -nt or -nct options ? Any recommendations regarding the parallelization ?

Comments

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    MuTect2 supports the same options as HaplotypeCaller. If I remember correctly, the original MuTect supported the same options as UnifiedGenotyper (so -nt and -nct) but I'm note 100% sure. Easiest way to be sure is try it on a snippet...

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