Issue with Running MuTect in GATK Version Compatibility

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김수영

• August 31, 2023 06:44

Hello GATK community,

I'm encountering an issue while trying to run MuTect using GATK and I need some guidance to resolve it. I'm currently using GATK version 4.4.0.0 for my analysis.

I am attempting to run MuTect using the following command:

mutect -T MuTect

However, I am receiving the following error message:

ERROR MESSAGE: Invalid command line: Malformed walker argument: Could not find walker with name: MuTect

It seems that the MuTect walker is not recognized by my current GATK version. I've checked the GATK documentation and forums, but I couldn't find any information regarding this issue. I've also tried using the --list command to list available walkers, but "MuTect" is not listed.

Could you please clarify whether MuTect is supported in GATK version 4.4.0.0 or suggest an alternative approach for MuTect? 

Thank you for your assistance.

Best regards,

Sooyoung

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• Official comment

  

  Gökalp Çelik

  • August 31, 2023 08:38
  • Edited

  Hi 김수영

  Mutect2 is present under GATK 4.4.0.0 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 hub.docker.com under tag

  broadinstitute/gatk:4.4.0.0

  I hope this helps. 

   

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• 

  김수영

  • September 01, 2023 01:24

  Hello,

  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 4.4.0.0, 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,
  Sooyoung

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  Gökalp Çelik

  • September 01, 2023 11:15

  Hi 

  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

  https://storage.googleapis.com/gatk-software/package-archive/mutect/mutect-1.1.7.jar 

  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. 

  Regards. 

   

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