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
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 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]