VarScan Overview

VarScan performs variant detection for massively parallel sequencing data, such as exome, WGS, and transcriptome data. It calls variants from a mpileup dataset and produces a VCF 4.1 Full documentation is available online.

Input

mpileup file - The SAMtools mpileup file

Output

VarScan produces a VCF 4.1 dataset as output.

Parameters

analysis type
  single nucleotide detection     Identify SNPs from an mpileup file
  insertions and deletion       Identify indels an mpileup file
  consensus genotype     Call consensus and variants from an mpileup file

min-coverage
  Minimum read depth at a position to make a call [8]

min-reads2
  Minimum supporting reads at a position to call variants [2]

min-avg-qual
  Minimum base quality at a position to count a read [15]

min-var-freq
      Minimum variant allele frequency threshold [0.01]

min-freq-for-hom
  Minimum frequency to call homozygote [0.75]

p-value
  Default p-value threshold for calling variants [99e-02]

strand-filter
  Ignore variants with >90% support on one strand [1]

output-vcf
  If set to 1, outputs in VCF format

vcf-sample-list
  For VCF output, a list of sample names in order, one per line

variants
  Report only variant (SNP/indel) positions [0]