This is the command varscan that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator
PROGRAM:
NAME
varscan - variant detection in next-generation sequencing data
SYNOPSIS
varscan [COMMAND] [OPTIONS]
DESCRIPTION
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.
USAGE
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
Use varscan online using onworks.net services
