Pittsburgh Supercomputing Center 

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VarScan

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. (2012). VarScan 2: Somatic mutation and copy number alteration discovery in cancer by exome sequencing Genome Research DOI: 10.1101/gr.129684.111
  • Website: http://varscan.sourceforge.net

Running VarScan

  1. Make VarScan availiable for use
    On blacklight:
    The VarScan program will be made availiable for use through the module command. To load the VarScan module enter:module load VarScan
  2. General Usage: java -jar $VARSCAN_HOME/VarScan.jar [COMMAND] [OPTIONS]

    Valid [COMMANDS] are:

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

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