Introduction

http://varscan.sourceforge.net/

Installing VarScan
The new release (VarScan 2) is written in Java and thus runs on any operating system (Linux, UNIX, Mac OSX, even Windows) through the Java Virtual Machine. To install it, run VarScan from the command line:

java -jar VarScan.v2.2.jar

Usage information will be displayed. For details on using VarScan, please see the User's Manual.
Documentation: http://varscan.sourceforge.net/doc/index.html

Usage

 module load bioinformatics/VarScan/2.2.11

Installation

mkdir /sw/bioinformatics/VarScan
cd /sw/bioinformatics/VarScan
ls
VarScan.v2.2.11.jar

java -jar VarScan.v2.2.11.jar
VarScan v2.3

USAGE: java -jar VarScan.jar [COMMAND] [OPTIONS]

COMMANDS:
        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