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

Versions

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.

Publisher/Vendor/Repository and License Type

http://varscan.sourceforge.net, Open source

Usage

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

Supercomputer: 
Service: 
Fields of Science: