VarScan

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. THE LATEST VERSION IS AVAILABLE ON GITHUB

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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License

Non-Profit Open Software License 3.0 (Non-Profit OSL 3.0)

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VarScan Web Site

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marcophoenix Posted 2013-06-06

Very useful. Thanks.

1 user found this review helpful.
fgiorgi Posted 2012-05-10

Great tool. This guy is a genius!
dkoboldt Posted 2010-01-22

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

Additional Project Details

Intended Audience

Science/Research

User Interface

Command-line

Programming Language

Java

Related Categories

Java Bio-Informatics Software

Registered

2010-01-13

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