VarScan Icon

VarScan

Variant detection in next-generation sequencing data

5.0 Stars (5)
119 Downloads (This Week)
Last Update:
Download VarScan.v2.3.9.jar
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Description

Variant detection in massively parallel sequencing. For one sample, calls SNPs, indels, and consensus genotypes. For tumor-normal pairs, further classifies each variant as Germline, Somatic, or LOH, and also detects somatic copy number changes.

VarScan Web Site

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
  • Free for non-commercial use.

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User Ratings

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User Reviews

  • 1 of 5 2 of 5 3 of 5 4 of 5 5 of 5

    Very useful. Thanks.

    Posted 06/06/2013
  • 1 of 5 2 of 5 3 of 5 4 of 5 5 of 5

    Great tool. This guy is a genius!

    Posted 05/10/2012
  • 1 of 5 2 of 5 3 of 5 4 of 5 5 of 5

    We use VarScan at the Genome Center at Washington University to call variants in Roche/454 and Illumina/Solexa data.

    Posted 01/22/2010
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Additional Project Details

Intended Audience

Science/Research

User Interface

Command-line

Programming Language

Java

Registered

2010-01-13

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