Now a days, genome or exome screening have become a norm in the conventional clinical analysis. However, pathogenic classification of the variants is still a manual, time consuming and tedious process for clicians or genticist. Thus, to facilitate the variant classification process, COMO - AI Lab, Vrije Universiteit Brussel along with CMG, UZ Brussel have developed GeVaCT, a Java based tool. Currently, GeVaCT version 1.0 is available, that can classify variants annotated by Alamut Batch Software, with a plan for future releases that support input file from other annotation software's also.

Authors acknowledge the support of BridgeIRIS project funded by INNOVIRIS, Region de Bruxelles Capitale, Brussels, Belgium.


  • GeVaCT is a standalone Java based tool. You need to download it from the resource link provided.
  • To install GeVaCT you need ~11.5 GB of hard disk space in your system. Ensure you have the specified space available in the drive you are planning to install.
  • To have GeVaCT running, ensure you have Java (version 6 or above) installed in your system, else download the latest version of Java, before proceding further.
  • Once the zipped file is downloaded, unzip the contents. Ensure you have a unzipping software like WinZIP or WinRAR, etc. installed in your system for this task.
  • When the given 'rar' file is unzipped, it will create a folder comprising of a executable jar file and a sqlite database.
  • Double click the jar file and you are ready to use the tool.


NOTE: GeVaCT Version 1.0 and sub-releases (1.01, 1.02, ...) can only be used for classifying variants with the input as annotated tab-delimited variant file (.vcf.ann) from the Alamut batch.


Watch the video for a quick preview of how to use GeVaCT for variant classification.



  1. Grau I., Daneels D., Van Dooren S., Bonduelle M., Md. Farid D., Croes D., Nowe A., and Sengupta D. (2015). GeVaCT: Genomic Variant Classifier Tool. 10th Benelux Bioinformatics Conference, Antwerp, Belgium, 7-8 Dec. 2015.
  2. Daneels D.(2016). Oral presentation: GeVaCT - genomic variant classifier tool. Laboratory Genetics Session at first joint meeting BeSHG/NVHG, Leuven, Belgium, 4-5 Feb. 2016.

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