DownloadVariant 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
Categories
Bio-InformaticsLicense
Non-Profit Open Software License 3.0 (Non-Profit OSL 3.0)Follow VarScan
You Might Also Like
Safetica is a cost-effective, easy-to-use Data Loss Prevention (DLP) solution. It performs security audits, prevents sensitive data from leaving your company, and sheds light on what is going on in your organization.
Rate This Project
Login To Rate This Project
User Reviews
-
Very useful. Thanks.
-
Great tool. This guy is a genius!
-
We use VarScan at the Genome Center at Washington University to call variants in Roche/454 and Illumina/Solexa data.