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The advent of massively parallel sequencing technologies has fundamentally changed the study of genetics. New platforms like the Illumina GAIIx and the Roche GS yield unprecedented levels of sequencing throughput. The analysis and interpretation of data from next-generation sequencing platforms presents a substantial informatics challenge.

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.

FEATURES:

· Calls SNPs and Indels from SAMtools pileup files
· Filters variants by coverage, read depth, variant frequency, and base quality
· Determines somatic status (Somatic, Germline, LOH) for Tumor-Normal pairs
· Compares, merges, and intersects two lists of variants
· Limits variant calls to a set of target positions or target regions