VarScan¶

Description¶

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

Additional Usage Information¶

VarScan software is contained in a platform-independent Java .jar file. Therefore, to run it call java as

java -Xmx<SIZE>g -jar $HPC_VARSCAN_DIR/VarScan.jar <command> <arguments>

or use the wrapper script we provide as

VarScan -Xmx<SIZE>g <command> <arguments>

Categories¶

biology, ngs