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Variant Discovery in High-Throughput Sequencing Data

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Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size. Learn more

Issue with Running MuTect in GATK Version Compatibility



  • Official comment
    Gökalp Çelik

    Hi 김수영

    Mutect2 is present under GATK and the correct syntax to call the tool would be 

    /path/to/gatk Mutect2 ... 

    Looking at the command that you use to call Mutect, it seems you are using a non-canonical way of calling GATK tools which we do not support. 

    Our suggestion is to use the latest version downloaded from the official github repository release page and using the gatk script provided with the java packages or using the docker container version available at under tag


    I hope this helps. 


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    Thank you for your prompt response. I understand that MuTect2 is recommended for variant calling, but I have specific reasons for needing to use MuTect in my analysis. I apologize for any confusion.

    Could you kindly provide guidance on how to correctly call and use the MuTect tool under GATK version, or alternatively, could you please let me know which GATK version supports the use of MuTect? I appreciate your assistance in helping me utilize MuTect for my analysis.

    Thank you,

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  • Avatar
    Gökalp Çelik


    If you are referring the original Mutect (Pre Mutect2) that you need for your analyses then the original Mutect is not part of any GATK package but it is available as a seperate tool named muTect. The latest release can be downloaded from the google cloud archive 

    Please keep in mind that this release is quite old and not supported anymore therefore any bugs or problems you may face while running this tool will not be fixed by our team. 



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