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


  • http://varscan.sourceforge.net
  • 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 get help and a list of VarScan commands, load the VarScan module

module load varscan

and then type

module help varscan

To run VarScan, include commands like these in your job script

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