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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: 1) germline variants (SNPs and indels) in individual samples or pools of samples, 2) multi-sample variants (shared or private) in multi-sample datasets (with mpileup), 3) somatic mutations, LOH events, and germline variants in tumor-normal pairs and 4) somatic copy number alterations (CNAs) in tumor-normal exome data.

Software type:
Package
Interface:
Command line interface
Restrictions to use:
None
Input format:
Pileup
Biological technology:
Illumina, Life Technologies, Pacific Biosciences, Roche
Operating system:
Unix/Linux, Mac OS, Windows
Programming languages:
Java, Perl, R
Computer skills:
Advanced
Version:
VarScan version 2.3.7
Stability:
Stable
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Institution(s)

Genome Institute at Washington University

  • (Koboldt et al., 2013) Using VarScan 2 for Germline Variant Calling and Somatic Mutation Detection. Current protocols in bioinformatics.
    PMID: 25553206
  • (Koboldt et al., 2012) VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing. Genome research.
    PMID: 22300766
  • (Koboldt et al., 2009) VarScan: variant detection in massively parallel sequencing of individual and pooled samples. Bioinformatics.
    PMID: 19542151
  • (Spencer et al., 2014) Performance of common analysis methods for detecting low-frequency single nucleotide variants in targeted next-generation sequence data. The Journal of molecular diagnostics.
    PMID: 24211364
  • (Stead et al., 2013) Accurately identifying low-allelic fraction variants in single samples with next-generation sequencing: applications in tumor subclone resolution. Human mutation.
    PMID: 23766071
  • (Roberts et al., 2013) A comparative analysis of algorithms for somatic SNV detection in cancer. Bioinformatics.
    PMID: 23842810
  • (Wang et al., 2013) Detecting somatic point mutations in cancer genome sequencing data: a comparison of mutation callers. Genome medicine.
    PMID: 24112718

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