varscan - variant detection in next-generation sequencing data

       Variant  detection  in  massively  parallel sequencing. For one sample, calls SNPs, indels, and consensus
       genotypes. For tumor-normal pairs, further classifies each variant as Germline, Somatic, or LOH, and also
       detects somatic copy number changes.

       varscan - variant detection in next-generation sequencing data

http://varscan.sourceforge.net/using-varscan.html

varscan 2.3.6                                      April 2014                                         VARSCAN(1)

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
              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