MuTect is a method developed at the Broad Institute for the reliable and accurate identification of somatic point mutations in next generation sequencing data of cancer genomes.

Availability and Restrictions


The following versions of MuTect are available on OSC clusters:

Version Owens
1.1.7 X*
* Current default version

You can use  module spider mutect to view available modules for a given machine. Feel free to contact OSC Help if you need other versions for your work.

Access for Academic Users

MuTect is available to academic OSC users. Please review the license agreement carefully before use. If you have any questions, please contact OSC Help.

Publisher/Vendor/Repository and License Type

The Broad Institute, Inc./ Freeware (academic)


Usage on Owens


To configure your environment for use of MuTect, run the following command: module load mutect. The default version will be loaded. To select a particular MuTect version, use module load mutect/version. For example, use module load mutect/1.1.4 to load MuTect 1.1.4.
NOTE: Java 1.7.0 will also need to be loaded in order to use MuTect: module load java/1.7.0.


This software is a Java executable .jar file; thus, it is not possible to add to the PATH environment variable.

From module load mutect, a new environment variable, MUTECT, will be set.

Thus, users can use the software by running the following command: java -jar $MUTECT {other options}.

Further Reading

Fields of Science: