VarScan Variant detection in massively parallel sequencing data
Download

VarScan Ranking & Summary

VarScan Tags

identify sequence snp identify snp sample seqeuencer snp identifier

VarScan Description

Variant detection in massively parallel sequencing data VarScan is a free and open source, platform-independent, technology-independent software tool for identifying SNPs and deals 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. Here are some key features of "VarScan": · 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 · Free for non-commercial use. Requirements: · Java

VarScan Related Software