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
Deploy Red Hat Ansible Automation Platform on Microsoft Azure for a strategic automation solution that allows you to orchestrate, govern and operationalize your Azure environment.
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.