varscan

variant detection in next-generation sequencing data

Install

All systems
curl cmd.cat/varscan.sh
Ubuntu
apt-get install varscan
image/svg+xml Kali Linux
apt-get install varscan
Windows (WSL2)
sudo apt-get update sudo apt-get install varscan
Dockerfile
dockerfile.run/varscan

varscan

variant detection in next-generation sequencing data

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.