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Does MuTect2 in gatk-4.0.3.0 support Nvidia Tesla 24 GBytes K80 Accelerator?

jingmengjingmeng AustraliaMember

Hi, I am using MuTect2 in gatk-4.0.3.0. Since the speed is slow, I am planning to use Nvidia Tesla 24 GBytes K80 Accelerator. Does MuTect2 support such GPU? If so, how can I set the parameter to let MuTect run on such GPU? Thank you!

Issue · Github
by Sheila

Issue Number
3033
State
closed
Last Updated
Assignee
Array
Closed By
droazen

Answers

  • jingmengjingmeng AustraliaMember

    If it does not support GPU, does it support multiple cores? Specifically, the speed of running on a 32 cores computer is the same as running on a computer of 8 cores? If it supports multiple cores, how to set the parameter to let MuTect use multiple cores? Thanks for your time!

  • SheilaSheila Broad InstituteMember, Broadie ✭✭✭✭✭
    edited April 2018

    @jingmeng
    Hi,

    I need to check with the developer and get back to you.

    -Sheila

    EDIT: I heard back, and "No, neither HaplotypeCaller nor Mutect2 natively support GPU acceleration."

    Post edited by Sheila on
  • jingmengjingmeng AustraliaMember

    Thanks. Does MuTect2 support multiple cores? Specifically, the speed of running on a 32 cores computer is the same as running on a computer of 8 cores? If it supports multiple cores, how to set the parameter to let MuTect use multiple cores? Thanks for your time!

  • SheilaSheila Broad InstituteMember, Broadie ✭✭✭✭✭

    @jingmeng
    Hi,

    I am checking with the developer and will get back to you.

    -Sheila

  • SheilaSheila Broad InstituteMember, Broadie ✭✭✭✭✭

    @jingmeng
    Hi again,

    Sorry for the delay. From the developer:

    "Mutect2 does not currently support multiple cores, with the exception of the AVX_LOGLESS_CACHING_OMP PairHMM, which accepts a --native-pair-hmm-threads argument that currently defaults to 4 threads. The GATK uses this PairHMM by default whenever the OpenMP library is installed and the CPU supports the AVX instruction set."

    -Sheila

  • shleeshlee CambridgeMember, Broadie ✭✭✭✭✭

    Just to add one note @jingmeng. GPU compatibility in GATK4 is limited to our CNN workflow, which is currently experimental. You can explore the resources related to the workflow at https://github.com/broadinstitute/dsde-deep-learning.

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