What it does

VarScan is a platform-independent mutation caller for targeted, exome, and whole-genome resequencing data generated on Illumina, SOLiD, Life/PGM, Roche/454, and similar instruments. The newest version, VarScan 2, is written in Java, so it runs on most  operating systems. It can be used to detect different types of variation:

   Germline variants (SNPs an dindels) in individual samples or pools of samples.
   Multi-sample variants (shared or private) in multi-sample datasets (with mpileup).
   Somatic mutations, LOH events, and germline variants in tumor-normal pairs.
   Somatic copy number alterations (CNAs) in tumor-normal exome data.

Input

mpileup normal file - The SAMtools mpileup file for normal
mpileup tumor file - The SAMtools mpileup file for tumor

Parameters

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

min-coverage-normal
      Minimum coverage in normal to call somatic [8]

min-coverage-tumor
      Minimum coverage in tumor to call somatic [6]

min-var-freq
      Minimum variant frequency to call a heterozygote [0.10]

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

normal-purity
      Estimated purity (non-tumor content) of normal sample [1.00]

tumor-purity
      Estimated purity (tumor content) of tumor sample [1.00]

p-value
      Default p-value threshold for calling variants [0.99]

somatic-p-value
      P-value threshold to call a somatic site [0.05]

strand-filter
      If set to 1, removes variants with >90% strand bias

validation
      If set to 1, outputs all compared positions even if non-variant

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