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
File search patterns
varscan2/mpileup2snp: contents: Only SNPs will be reported num_lines: 3 varscan2/mpileup2indel: contents: Only indels will be reported num_lines: 3 varscan2/mpileup2cns: contents: Only variants will be reported num_lines: 3