MuTect

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 Oakley owens
1.1.4 X  
1.1.7 X* 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 with proper validation. In order to obtain validation, please contact OSC Help for further instruction. 

Usage on Oakley

Set-up

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 will also need to be loaded in order to use MuTect: module load java

Usage

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}

Usage on Owens

Set-up

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

Usage

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

Service: 
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