How to get sample coverage files in WIG (wiggle) format using gatk Mutect

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chenglei

• October 30, 2021 07:07

When I use MutSigCV to call significantly mutated genes, a coverage file was required. As pointed by the document of MutSigCV, this coverage file can be deriveed from processing sample coverage files in WIG (wiggle) format output by Mutect. Could you tell me How to get sample coverage files in WIG (wiggle) format using gatk Mutect.

https://www.genepattern.org/modules/docs/MutSigCV

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  Pamela Bretscher

  • November 05, 2021 13:48

  Hi chenglei,

  The GATK team no longer supports MuTect which uses different algorithms and models than the current MuTect2. I don't believe MuTect2 is applicable to this MutSigCV pipeline. However, the document you referenced does link to this document explaining how to use MuTect and the files it outputs which you might find helpful. There may be other users on the forum who can provide more insight into these pipelines.

  Kind regards,

  Pamela

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