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 frequencyh. 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.
The Genome Institute at Washington University
- Linux / Windows / Mac OsX
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Koboldt DC, Chen K, Wylie T, Larson DE, McLellan MD, Mardis ER, Weinstock GM, Wilson RK, & Ding L (2009).
VarScan: variant detection in massively parallel sequencing of individual and pooled samples.
Bioinformatics (Oxford, England), 25 (17), 2283-5 PMID: