SNVerGUI is a desktop tool for variant detection from next generation sequencing data, which has unique features: 1) Platform-free compatibility; 2) Support all standard inputs and outputs; 3) Omnibus variant calling; 4) Flexible interactive post-call processing. With SNVerGUI, the users can run the entire variant calling pipeline after simply configuring several parameters via the user-friendly GUI. Moreover, SNVerGUI displays the results as a typical table view supporting various interactive filtering and sorting. It also generates an automatic summary report for further analysis.

SNVerGUI is a graphical user interface version of SNVer tool. It has following unique features:

1) Platform-free compatibility. The java-based SNVerGUI inherits the natural merit of Java property with its “write once, run anywhere” concept. The program is wrapped in “one-click” installation and runs on most common operating systems, such as Windows, Linux, and Mac and Windows. The users can configure proper parameters and process high volume data in their local machines.

2) Support all standard inputs and outputs. SNVerGUI accepts local reads data and reference sequence data in all standard file formats, such as .fasta, .sam and .bam files. Variant detection results are output in the standard VCF (Variant Call Format). The tool works seamlessly with commonly used programs such as Excel and SAMTools etc.

3) Omnibus variant calling. SNVerGUI can call SNVs from both pooled and individual NGS data by a unified binomial-binomial statistical model. It can handle single-pool NGS data, which cannot be processed by most, if not all, existing state-of-the-art tools. Its computing efficiency makes it feasible to analyze whole-exome or whole-genome NGS data.

4) Flexible interactive post-call processing. Variants can be viewed as tables, supporting various interactive sorting and filtering. Users can easily customize the outputs for their needs based on their domain knowledge and/or desired multiplicity control.

Binary Downloads

   Windows (win32/x86_64)
   Windows (win32/x86)
   Mac OSX (cocoa/x86_64)
   Mac OSX (cocoa/x86)
   Linux (gtk/x86_64)
   Linux (gtk/x86)


Please refer to HelpManual.pdf for tutorial and getting help.

Sample Data

Please download Sample Data to get started.


Support is provided through SNVer Mailing Lists.