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 |
