VarScan USAGE: java -jar VarScan.jar [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…