VarScan

Overview
Installation
Usage
Citing VarScan
License Information

OVERVIEW

VarScan is a platform-independent, technology-independent software tool for identifying SNPs and indels in massively parallel sequencing of individual and pooled samples. Given data for a single sample, VarScan identifies and filters germline variants based on read counts, base quality, and allele frequency. Given data for a tumor-normal pair, VarScan also determines the somatic status of each variant (Germline, Somatic, or LOH) by comparing read counts between samples. For more information, please visit the VarScan page on Sourceforge.net.

INSTALLATION

The new release (VarScan 2) is written in Java and thus runs on any operating system (Linux, UNIX, Mac OSX, even Windows) through the Java Virtual Machine. To install it, you must download the VarScan JAR file from SourceForge. Then, run VarScan from the command line:

java -jar VarScan.v2.2.jar

Usage information will be displayed.

USAGE

VarScan functions can be accessed through several sub-commands in this syntax:

java -jar VarScan.v2.2.jar [COMMAND] [OPTIONS]

COMMANDS:

Variant Calling

    pileup2snp       Identify SNPs from a pileup file
    pileup2indel     Identify indels a pileup file
    pileup2cns       Call consensus and variants from a pileup file
    somatic          Call germline/somatic variants from tumor-normal pileups
    processSomatic   Isolate Germline/LOH/Somatic calls from output
    readcounts       Obtain read counts for a list of variants from a pileup file

Filtering

    filter           Filter SNPs by coverage, frequency, p-value, etc.
    somaticFilter    Filter somatic variants for clusters/indels

Comparison

    compare          Compare two lists of positions/variants
    limit            Restrict pileup/snps/indels to ROI positions

Experimental

    copyCaller       Call copy number changes from somatic copy number output

For details on using VarScan, please see the User's Manual.

CITING VARSCAN

Please use the following publication and URL to cite VarScan:

Koboldt DC, Chen K, Wylie T, Larson DE, McLellan MD, Mardis ER, Weinstock GM, Wilson RK, & Ding L (2009). VarScan: variant detection in massively parallel sequencing of individual and pooled samples. Bioinformatics (Oxford, England), 25 (17), 2283-5 PMID: 19542151
URL: http://varscan.sourceforge.net

LICENSE INFORMATION

VarScan is free for non-commercial use. For details on commercial licensing, please contact Dan Koboldt at dkoboldt (at) genome (dot) wustl (dot) edu.