VarScan

VarScan is a platform-independent software tool developed at the Genome Institute at Washington University to detect variants in NGS data.

Availability and Restrictions

The following versions of VarScan are available on OSC clusters:

Version Oakley Owens
2.4.1 X* X*
*: Current default version

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

Access

VarScan is available to all OSC users without restriction.

Usage on Oakley

Set-up

To configure your environment for use of VarScan, run the following command:   module load varscan. The default version will be loaded. To select a particular VarScan version, use   module load varscan/version . For example, use  module load varscan/2.4.1 to load VarScan 2.4.1.

Usage

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

From module load varscan , a new environment variable, VARSCAN, will be set.

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

Usage on Owens

Set-up

To configure your environment for use of VarScan, run the following command:   module load varscan. The default version will be loaded. To select a particular VarScan version, use   module load varscan/version . For example, use  module load varscan/2.4.1 to load VarScan 2.4.1.

Usage

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

From module load varscan , a new environment variable, VARSCAN, will be set.

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

Further Reading

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