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