VarScan

Description

varscan website

VarScan is a platform-independent mutation caller for targeted, exome, and whole-genome resequencing data generated on Illumina, SOLiD, Life/PGM, Roche/454, and similar instruments. The newest version, VarScan 2, is written in Java, so it runs on most operating systems. It can be used to detect different types of variation: - Germline variants (SNPs an dindels) in individual samples or sample pools. - Multi-sample variants (shared or private) in multi-sample datasets (with mpileup). - Somatic mutations, LOH events, and germline variants in tumor-normal pairs. - Somatic copy number alterations (CNAs) in tumor-normal exome data. Note: We provide a VarScan wrapper script that calls java with the correct jar file.

Environment Modules

Run module spider varscan to find out what environment modules are available for this application.

Environment Variables

• HPC_VARSCAN_DIR - software directory

Categories

biology, ngs