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mutations of Mutect2 gatk- are very different from gatk-3.0

We used mutect2 gatk- and compared results the older version 3.0 results with 16 samples, the filter results are different with older more than 90%. The raw results are more than 70% different.
Bam are the same.
where are differences between with the two versions?
Thank you !



  • SkyWarriorSkyWarrior TurkeyMember ✭✭✭
    edited April 2018

    Can you perform a GenotypeConcordance test and paste the results here?

    My HaplotypeCaller results are not that different (less than 0.01 difference at marginal variants mostly false positives.)

    Also Mutect2 in GATK3.0 is not considered ready for production. Mutect2 in GATK4.0 is more mature

  • SheilaSheila Broad InstituteMember, Broadie ✭✭✭✭✭


    the filter results are different with older more than 90%.

    Can you post some examples where there are differences?

    The tools are definitely more evolved in GATK4 and out of beta. I know the team has been making many changes, so you would have to look through the release notes to find which may have caused your differences. Also, can you post a few examples where the raw results are different from GATK3 to GATK4?


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