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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

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


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    Pamela Bretscher

    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,


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