varscan online with Winfy

We have hosted the application varscan in order to run this application in our online workstations with Wine or directly.

Quick description about 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.

Audience: Science/Research.
User interface: Command-line.
Programming Language: Java.
Categories: