WashU Analysis Tools
Short Read Aligners
VarScan OverviewThe 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?
Release Notes and Announcements
- 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.
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 MutationsA 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.
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.
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
|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).|