VarScan

VarScan Overview

The advent of massively parallel sequencing technologies has fundamentally changed the study of genetics. New platforms like the Illumina HiSeq2000 yield unprecedented levels of sequencing throughput. The analysis and interpretation of data from next-generation sequencing (NGS) platforms presents a substantial informatics challenge. VarScan is a platform-independent software tool developed at the Genome Institute at Washington University to detect variants in NGS data.
Sequencing Platforms and Variant Types
Why Use VarScan?
Installing VarScan
Citing VarScan
Release Notes and Announcements

Sequencing Platforms and Variant Types

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 pools of samples.
• 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.

Why Use VarScan?

Most of the published variant callers for next-generation sequencing data employ a probabilistic framework, such as Bayesian statistics, to detect variants and assess confidence in them. These approaches generally work quite well, but can be confounded by numerous factors such as extreme read depth, pooled samples, and contaminated or impure samples. In contrast, VarScan employs a robust heuristic/statistic approach to call variants that meet desired thresholds for read depth, base quality, variant allele frequency, and statistical significance.

VarScan is under continued development and improvement at a leading genome center with early access to new sequencing technologies, substantial computing resources, immense public/private datasets, and established expertise in sequencing, genetics, and genomics.

Detecting Subclonal Mutations

A 2013 study by Stead et al evaluated several somatic mutation callers including MuTect, Strelka, and VarScan2. They found that VarScan2 performed best overall with sequencing depths of 100x, 250x, 500x and 1000x required to accurately identify variants present at 10%, 5%, 2.5% and 1% respectively.

Installing VarScan

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.jar

Usage information will be displayed. For details on using VarScan, please see the User's Manual.

Citing VarScan

Please note the version number, and cite the publications below with URL to cite VarScan:

VarScan 1: 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 VarScan 2: Koboldt, D., Zhang, Q., Larson, D., Shen, D., McLellan, M., Lin, L., Miller, C., Mardis, E., Ding, L., & Wilson, R. (2012). VarScan 2: Somatic mutation and copy number alteration discovery in cancer by exome sequencing Genome Research DOI: 10.1101/gr.129684.111 URL: http://varscan.sourceforge.net

Release Notes

04-29-2015		VarScan v2.3.8 released with fpfilter integration. This expands and replaces the functionality of the fpfilter.pl accessory script.
07-15-2014		VarScan v2.3.7 released with SAMtools 0-depth fixes. This should address crashes or missing columns due to sites with 0 depth in the SAMtools mpileup output.
01-30-2013		VarScan v2.3.4 released with better VCF compatibility. You can now specify a file of ordered sample names for multi-sample variant calling.
08-09-2012		VarScan v2.3.1 released with bug fixes, extended VCF compatibility, and more copynumber calling features.. Multi-sample VCF output now has quality scores.
05-01-2012		VarScan v2.2.11 released with base quality parsing fix and VCF output option for somatic mutations.
03-23-2012		VarScan v2.2.10 released with documentation, VCF column order, and somaticFilter fixes.
02-29-2012		Happy Leap Day: User's manual and documentation updated to cover mpileup/multi-sample calling, somatic CNA detetion, and other items.
02-03-2012		VarScan 2 published in Genome Research with demonstration of somatic mutation and copy number alteration calling.
10-14-2011		VarScan v2.2.8 released with new somatic calling features: Tumor-normal mpileup compatibility and VCF 4.1 output option.
08-16-2011		VarScan v2.2.7 released with copyCaller post-processing, mpileup compatibility for multiple-sample calling, and VCF 4.0 output option.
07-29-2011		New VarScan copynumber function for identifying copy number changes in tumor-normal exome pairs. See the copy number calling section for details.
04-29-2011		New Support FAQ launched! Find answers to frequently-asked questions about VarScan usage, parameters, input/output, and other topics.
04-28-2011		VarScan v2.2.5 released! New features include normal and tumor purity input parameters for somatic mutation calling, which can improve sensitivity for genomes with reduced tumor cellularity, or matched normal samples that contain some tumor cells (e.g. leukemias).