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.

Project Samples

Project Activity

See All Activity >

License

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

Follow VarScan

VarScan Web Site

Other Useful Business Software

Get full visibility and control over your tasks and projects with Wrike.

A cloud-based collaboration, work management, and project management software

Wrike offers world-class features that empower cross-functional, distributed, or growing teams take their projects from the initial request stage all the way to tracking work progress and reporting results.

Learn More

Rate This Project

User Ratings

5.0 out of 5 stars

★★★★★

★★★★

★★★

★★

★

ease 1 of 5 2 of 5 3 of 5 4 of 5 5 of 5 0 / 5

features 1 of 5 2 of 5 3 of 5 4 of 5 5 of 5 0 / 5

design 1 of 5 2 of 5 3 of 5 4 of 5 5 of 5 0 / 5

support 1 of 5 2 of 5 3 of 5 4 of 5 5 of 5 0 / 5

User Reviews

Filter Reviews:

All

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

Similar Business Software

Genome Analysis Toolkit (GATK)

Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size. The GATK...

See Software
Geneious

Geneious Prime makes bioinformatics accessible by transforming raw data into visualizations that make sequence analysis intuitive and user-friendly. Simple sequence assembly and easy editing of contigs. Automatic annotation for gene prediction, motifs, translation, and variant calling. Genotype...

See Software
Illumina DRAGEN Secondary Analysis

The Illumina DRAGEN Secondary Analysis provides accurate, comprehensive, and efficient analysis of next-generation sequencing data. Graph reference genome and machine learning driving unprecedented accuracy. Provides ultra-efficient workflow; can fully process a 34x whole human genome in ~30...

See Software
SeqOne

SeqOne is an AI-powered genomic analysis platform designed to help molecular laboratories, clinical teams, biologists, and geneticists transform complex next-generation sequencing data into fast, precise, and actionable clinical insights to support personalized medicine diagnostics. It...

See Software
GenomeBrowse

This free tool delivers stunning visualizations of your genomic data that give you the power to see what is occurring at each base pair in your samples. GenomeBrowse runs as a native desktop application on your computer. No longer do you have to sacrifice speed and interface quality to obtain a...

See Software
Alissa Interpret

Alissa Interpret is your universal genomic data interpretation software for clinical decision support. Increase your productivity, shorten the turnaround time, and maintain regulatory compliance with Alissa Interpret’s agnostic CGH and NGS tertiary analysis platform for variant interpretation...

See Software