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Uses for the variant matching problem. VarMatch is able to detect more matches than either the normalization or decomposition algorithms on tested datasets. It is robust to different representation of complex variants and is particularly effective in low complexity regions or those dense in variants. It also implements different optimization criteria, such as edit distance, that can improve robustness to different variant representations. Finally, the VarMatch software provides summary statistics, annotations, and visualizations that are useful for understanding callers’ performance

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It's especially useful to find high-quality variants by intersecting the results of different variant calling tools. For instance, you can predict variants using Freebayes and GATK, and then use VarMatch to find high-quality variants that are supported by both tools.

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VarMatch classification

VarMatch specifications

Software type:
Restrictions to use:
Operating system:
Unix/Linux, Mac OS, Windows
GNU General Public License version 3.0
Command line interface
Input format:
Programming languages:
C++, Python
Computer skills:
GCC, matplotlib

VarMatch distribution


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VarMatch support



  • Chen Sun <>


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Department of Computer Science and Engineering, The Pennsylvania State University, PA, USA; Department of Biochemistry and Molecular Biology, The Pennsylvania State University, PA, USA; Genome Sciences Institute at the Huck, The Pennsylvania State University, PA, USA

Funding source(s)

This work has been supported in part by NSF awards DBI-1356529, CCF-1439057, IIS-1453527, and IIS-1421908.

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