Varscan

VARSCAN

Record added by Jurg Ott (the original Rockefeller list)

Description

VarScan is a platform-independent, technology-independent software tool for identifying SNPs and indels in massively parallel sequencing of individual and pooled samples. Given data for a single sample, VarScan identifies and filters germline variants based on read counts, base quality, and allele frequency. Given data for a tumor-normal pair, VarScan also determines the somatic status of each variant (Germline, Somatic, or LOH) by comparing read counts between samples.

URL

http://genome.wustl.edu/software/varscan

Language

Java

Reference

Koboldt, Chen, Wylie, Larson, McLellan, Mardis, Weinstock, Wilson, Ding (2009), “VarScan: variant detection in massively parallel sequencing of individual and pooled samples”, Bioinformatics, 25:2283-2285.