MuTect was a variant caller built on top of GATK and specialized for somatic/cancer variants, originally developed by our collaborators from the Cancer Genome Analysis program here at the Broad Institute. This is the last original standalone MuTect version 1, which is limited to calling SNVs.
A beta version of Mutect2, the next generation somatic SNP and indel caller, is included in GATK starting from version 3.5. For best results, use the version of Mutect 2 included in GATK4 versions beta.1 and above.
All POSIX operating systems (Unix, Linux, MacOSX etc) are supported. Microsoft Windows is not supported. The current version requires Java 1.8. Note that the Oracle Java is preferred; OpenJDK is not officially supported.
Both the original standalone MuTect and the beta version of MuTect2 included in GATK versions 3.x are available for free to academic researchers under a limited license for non-commercial use. The beta version of Mutect2 available in GATK versions 4.x is free for all uses under a BSD 3-clause open-source license. Please see the Licensing page for more information.
The MuTect 1 source code is available in the broadinstitute/mutect repository on Github. The first version of MuTect 2 beta source code (in GATK 3.x) is available in the broadgsa/gatk-protected repository on Github. The latest version of Mutect 2 source code (in GATK 4.x) is available in the broadinstitute/gatk repository on Github.