VarScan Easily identify SNPs with this application
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VarScan Description

VarScan is a Java-based tool that is specially designed to be a platform and technology-independent utility 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. Main 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

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