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memory requirements for MUTECT2/GATK

BogdanBogdan Palo Alto, CAMember ✭✭

Dear all,

please could you advise if there is any way to reduce the memory requirements for GATK/MUTECT2 (in GATK versions 3.5-3.8) ? Recently, we've started running MUTECT2 per chromosome on a SGE minicluster at UCSF, and it does not run unless we set 30GB per chromosome run.

thank you,

bogdan

Answers

  • shleeshlee CambridgeMember, Broadie ✭✭✭✭✭

    Hi @Bogdan,

    GATK4-beta-Mutect2 (tool is in beta) has improvements that lower the memory requirement.

    Which reference are you using? GRCh38 reduces memory burden. If you are using a prior assembly, then I suggest you use an intervals list to limit calling to non-problematic regions.

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