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. If you have any questions, please contact OSC Help.

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: