This is the Linux app named VarScan to run in Linux online 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.
Download and run online this app named VarScan to run in Linux online with OnWorks for free.
Follow these instructions in order to run this app:
- 1. Downloaded this application in your PC.
- 2. Enter in our file manager https://www.onworks.net/myfiles.php?username=XXXXX with the username that you want.
- 3. Upload this application in such filemanager.
- 4. Start the OnWorks Linux online or Windows online emulator or MACOS online emulator from this website.
- 5. From the OnWorks Linux OS you have just started, goto our file manager https://www.onworks.net/myfiles.php?username=XXXXX with the username that you want.
- 6. Download the application, install it and run it.
SCREENSHOTS
Ad
VarScan to run in Linux online
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 GITHUBFeatures
- 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
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.
