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mutect2 release date

I read that there is a new version of MuTect dealing with indels coming. Would it be possible to know its release date?
We are planning analyses for a new project and would like to know if we can count on MuTect2 or not.




  • Geraldine_VdAuweraGeraldine_VdAuwera admin Cambridge, MAMember, Administrator, Broadie admin

    It's a just matter of weeks now, though I can't give you an exact date as we're waiting on the last validation results from collaborators. If you're in the planning phase I think it's probably safe to count on MuTect2 to be out by the time you start processing data.

  • GumiltonGumilton United StatesMember


    Hi Geraldine,
    We have processed our samples with MuTect 1.1.7 and results came out good!
    But we have to use another tool for indel detection.
    I am wondering how soon we may see the release of MuTect2? Would you add me in the mailing list if there is one? Thanks!

    When I called java -jar mutect-1.1.7.jar --version
    It said 3.1-0-g72492bb
    What kind of version number is this? looks like version 3... not MuTect3...

    Xiang GU

  • Geraldine_VdAuweraGeraldine_VdAuwera admin Cambridge, MAMember, Administrator, Broadie admin

    That's the GATK version number that MuTect 1 is built on top of.

    The new MuTect is coming out very soon, we just hit a small technical problem that has delayed the release, but hopefully we'll get it out by the end of the week. (I know I keep saying that but it is the intention).

  • GumiltonGumilton United StatesMember

    Cool! Thanks!

  • himanandinihimanandini LondonMember

    I believe the new version is out now, I tried running Mutect version 1.1.7 using the standard CL but do not find indels to come up in my vcf file. Can you let me know if there is any additional option to include Indels?

  • Geraldine_VdAuweraGeraldine_VdAuwera admin Cambridge, MAMember, Administrator, Broadie admin

    Only MuTect2 calls indels. You can use it in GATK 3.5.

  • tinutinu Member

    Using MuTect2 for T:N variant calling using the following command

    java -Xmx8G -jar GATK-3.5/GenomeAnalysisTK.jar -T MuTect2 -R hs37d5.fa -I:tumor Tumor.bam -I:normal normal.bam --dbsnp dbsnp_138.b37.vcf -nct 2 --cosmicb37_cosmic_v54_120711.vcf -L interval.bed -o Tumor-Normal_MuTect2.vcf

    The normal bam is from exome sequenced data. The size of the bams are
    Tumor.bam (20G)
    Normal.bam (18G)

    MuTect2 has been running for 42.5 hours and only 7.7% of the runs got completed so far. Is there a way to make the runs faster ?


  • SheilaSheila admin Broad InstituteMember, Broadie, Moderator admin


    Your best bet is Queue.

    Also, have a look at this thread.


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