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
- Make VarScan availiable for use
The VarScan program will be made 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:
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