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

Running VarScan

1) Make VarScan availiable for use
a) 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
Last Updated on Saturday, 09 November 2013 18:12  

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