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VarScan

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.

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VarScan classification

VarScan specifications

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

VarScan distribution

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Publications

Institution(s)

Genome Institute at Washington University

Link to literature

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