VarScan download for Windows

This is the Windows app named VarScan whose latest release can be downloaded as VarScan.v2.3.9.jar. It can be run online in the free hosting provider OnWorks for workstations.

 
 

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- 7. Download Wine from your Linux distributions software repositories. Once installed, you can then double-click the app to run them with Wine. You can also try PlayOnLinux, a fancy interface over Wine that will help you install popular Windows programs and games.

Wine is a way to run Windows software on Linux, but with no Windows required. Wine is an open-source Windows compatibility layer that can run Windows programs directly on any Linux desktop. Essentially, Wine is trying to re-implement enough of Windows from scratch so that it can run all those Windows applications without actually needing Windows.

SCREENSHOTS:


VarScan


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. 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.


Audience

Science/Research


User interface

Command-line


Programming Language

Java


Categories

Bio-Informatics

This is an application that can also be fetched from https://sourceforge.net/projects/varscan/. It has been hosted in OnWorks in order to be run online in an easiest way from one of our free Operative Systems.



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