MuTect is 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 Broad. 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 the latest release of GATK (versions 3.5 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 are available for free to academic researchers under a limited license for non-commercial use. If you plan to use MuTect for-profit, you will need to purchase a license. Please see the Licensing page for more information. Note that MuTect2 is not currently available for commercial use due to its beta status.
The MuTect 1 source code is available in the broadinstitute/mutect repository on Github.