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 Owens
2.4.1 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.


VarScan is available to all OSC users without restriction.

Publisher/Vendor/Repository and License Type, Open source


Usage on Owens


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.


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

Fields of Science: