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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.

Installed on blacklight.

Other resources that may be helpful include:

  • 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
  • Website: http://varscan.sourceforge.net

Running VarScan

The VarScan program is availiable for use through the module command. To load the VarScan module enter

module load VarScan

General Usage

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


Valid [COMMANDS] are:

compare Compare two lists of positions/variants
copyCaller GC-adjust and process copy number changes from VarScan copynumber output
copynumber Determine relative tumor copy number from tumor-normal pileups
filter Filter SNPs by coverage, frequency, p-value, etc.
limit Restrict pileup/snps/indels to ROI positions
mpileup2cns Call consensus and variants from an mpileup file
mpileup2indel Identify indels an mpileup file
mpileup2snp Identify SNPs from an mpileup file
pileup2cns Call consensus and variants from a pileup file
pileup2indel Identify indels a pileup file
pileup2snp Identify SNPs from a pileup file
processSomatic Isolate Germline/LOH/Somatic calls from output
readcounts Obtain read counts for a list of variants from a pileup file
somatic Call germline/somatic variants from tumor-normal pileups
somaticFilter Filter somatic variants for clusters/indels