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


  • Koboldt, D., Zhang, Q., Larson, D., Shen, D., McLellan, M., Lin, L., Miller, C., Mardis, E., Ding, L., & Wilson, R,  VarScan 2: Somatic mutation and copy number alteration discovery in cancer by exome sequencing. Genome Research (2012). DOI: 10.1101/gr.129684.111

Usage on Bridges


To see what other modules are needed, what commands are available and how to get additional help type

module help varscan


To see what versions of VarScan are available type

module avail varscan


To use VarScan, include a command like this in your batch script or interactive session to load the VarScan module:

module load varscan

Be sure you also load any other modules needed, as listed by the module help varscan command.


The general version of the VarScan command is

java -jar $VARSCAN_HOME/VarScan.jar [COMMAND] [OPTIONS]


See more about VarScan