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What are the platform requirements and software dependencies for running MuTect?
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.
MuTect is based on the GATK, and has the same requirements: Java 1.7 (it must be the Sun JDK as OpenJDK is not supported) on MacOSX, Linux or other Unix/POSIX platform. Microsoft Windows systems are not supported at this time.