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Please note that this article refers to the original standalone version of MuTect. A new version is now available within GATK (starting at GATK 3.5) under the name MuTect2. This new version is able to call both SNPs and indels. See the GATK version 3.5 release notes and the MuTect2 tool documentation for further details.
The MuTect source code is now available as a GitHub repository (https://github.com/broadinstitute/mutect). If you wish to build from source, please read the build instructions carefully as we are currently building against a tag (v2.5) of the gatk-protected repository. We'll be moving to 2.6 soon (which is based on Java 7). We'll be doing some cleanup as we move from our internal source control and environment to a more open environment, but wanted to make the code available sooner rather than later.
Of course, please make sure that you abide by the terms of the license agreement which is in each file header as well as in the GitHub repository https://github.com/broadinstitute/mutect/blob/master/mutect.LICENSE.TXT
Thanks, and please let us know if you find any problems