varscan - variant detection in next-generation sequencing data
varscan [COMMAND] [OPTIONS]
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.
- 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
http://varscan.sourceforge.net/using-varscan.html