VarScan on Helix
VarScan is a platform-independent, technology-independent software tool for identifying SNPs and indels in massively parallel sequencing of individual and pooled samples. Given data for a single sample, VarScan identifies and filters germline variants based on read counts, base quality, and allele frequency. Given data for a tumor-normal pair, VarScan also determines the somatic status of each variant (Germline, Somatic, or LOH) by comparing read counts between samples.
/usr/local/VarScan/VarScan.jarJar files for all available versions of VarScan are located in this directory. /usr/local/VarScan/VarScan.jar is a link to the latest version.
VersionRunning the Varscan command as below with no options will print a usage message that includes the version.
Enter java -jar /usr/local/VarScan/VarScan.jar to see a list of Varscan options.
[user@helix ]$ java -jar /usr/local/VarScan/VarScan.jar VarScan v2.2 USAGE: java net.sf.varscan.VarScan [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 Call copy number changes from somatic copy number output compare Compare two lists of positions/variants limit Restrict pileup/snps/indels to ROI positions