Record added by Jurg Ott (the original Rockefeller list)
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.
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.