VarScan 2 Released on SourceForge

Accurate variant detection in massively parallel sequencing data is a significant bioinformatics challenge. Not only do new sequencers offer unprecedented breadth (whole genome) and depth (30x or more), but they suffer coverage biases and error rates that make variant calling difficult. Last year, we published VarScan, our in-house algorithm for SNP and indel detection on next-generation platforms. NGS analysis has changed somewhat since that time; SAM/BAM format was widely adopted, for one thing, and data throughput has skyrocketed.

To address these issues as well as the requests of many users, we have released VarScan 2 on The new version features many improvements and enhancements, including:

  • SAM/BAM compatibility. Rather than reading various native alignment formats, VarScan now accepts as input the “pileup” format of SAMtools. Since most widely used aligners can be converted to SAM format or output it directly, this makes VarScan compatible with a wide array of tools.
  • Java implementation. To increase speed and performance in the face of ever-increasing sequencing throughput, we’ve implemented the new VarScan in Java. This also means that it can run on any operating system through the Java virtual machine (VM).
  • New filtering and comparison tools. VarScan 2 now has commands to limit variants to a list of positions or chromosomal regions, which is useful for targeted sequencing projects. It also has a comparison tool that intersects or merges two sets of variants.
  • Somatic variant detection. This is the flagship feature of VarScan 2 – given pileup files from a tumor sample and matched control (normal), VarScan calls variants (SNPs and indels) and determines their somatic status (Germline, Somatic, LOH) using heuristic and statistical approaches.

Software and Documentation on

VarScan joins the ranks of some of the most widely used tools for NGS analysis – Bowtie, Maq, BWA, SAMtools, and Picard – that are hosted on The download page, user’s manual, and Java documentation for VarScan are already online. There’s a new wiki site and discussion forum for VarScan as well, to help us developers keep in touch with users and the NGS community. The project page will have information about known issues and new software releases.

You’ll find it all at


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

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German Leparc
German Leparc

Hi Dan,

what do you use to filter our germline variants from dbSNP ? I'm talking just a simple filter. Do you have any suggestions? I am looking for a simple command line based solution.

Looking forward to trying out your latest version of VarScan!

Dan Koboldt
Dan Koboldt


It was on the project page, but I added it to the main SF page: free for non-commercial use.

Keith Robison
Keith Robison

What license is this under? I'm probably being blind, but I don't see anything in the documentation.