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Supported Tool

Variant detection in massively parallel sequencing data


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.

VarScan 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.

The MultiQC module can read output from mpileup2cns, mpileup2snp and mpileup2indel logfiles.

File search patterns

  contents: Only SNPs will be reported
  num_lines: 3
  contents: Only indels will be reported
  num_lines: 3
  contents: Only variants will be reported
  num_lines: 3