to get the same results, must add -pairHMM LOGLESS_CACHING when I use the GATK 4.beta.4

Dear Dr. Geraldine
I have read https://gatkforums.broadinstitute.org/gatk/discussion/comment/40473#Comment_40473 about the reproduce questions. And I want to ask weather I must add -pairHMM LOGLESS_CACHING if i want to get the same result by the GATK version 4.beta.4.

Best Answer

  • SheilaSheila Broad Institute admin
    edited November 2017 Accepted Answer

    @Wqx_55
    Hi,

    Yes, I think you do need to use -pairHMM LOGLESS_CACHING in GATK4. However, I will confirm with the team and let you know for sure asap.

    -Sheila

    EDIT: I have confirmation that you do need to use it :smile:

    Post edited by Sheila on

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