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