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 18.104.22.168 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 22.214.171.124 or suggest an alternative approach for MuTect?
Thank you for your assistance.
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