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 | Owens |
|---|---|
| 2.4.1 | X* |
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. If you have any questions, please contact OSC Help.
Publisher/Vendor/Repository and License Type
http://varscan.sourceforge.net, Open source
Usage
Usage on Owens
Set-up
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}.
