The Exomiser

The Exomiser is a Java program that functionally annotates variants from whole-exome sequencing data starting from a VCF file (version 4). The functional annotation code is based on Jannovar and uses UCSC KnownGene transcript definitions and hg19 genomic coordinates.

Variants are prioritised according to user-defined criteria on variant frequency, pathogenicity, quality, inheritance pattern, and model organism phenotype data. Predicted pathogenicity data was extracted from the dbNSFP resource. Cross-species phenotype comparisons come from our PhenoDigm tool powered by the OWLSim algorithm.

The Exomiser was developed by the Computational Biology and Bioinformatics group at the Institute for Medical Genetics and Human Genetics of the Charité - Universitätsmedizin Berlin, the Mouse Informatics Group at the Sanger Institute and other members of the Monarch initiative.

An online version of the exomiser can be found here.

[Genome Research Limited]


FTP downloads

The Exomiser and supporting files can be downloaded from our FTP site. For instructions on installing and running please refer to the file.


How do I install and run exomiser from the command line?
Download exomiser from the FTP site and follow the instructions contained in the file.


  • Walking the interactome for candidate prioritization in exome sequencing studies of Mendelian diseases.

    Smedley D, Köhler S, Czeschik JC, Amberger J, Bocchini C, Hamosh A, Veldboer J, Zemojtel T and Robinson PN

    Bioinformatics (Oxford, England) 2014;30;22;3215-22

  • Effective diagnosis of genetic disease by computational phenotype analysis of the disease-associated genome.

    Zemojtel T, Köhler S, Mackenroth L, Jäger M, Hecht J, Krawitz P, Graul-Neumann L, Doelken S, Ehmke N, Spielmann M, Oien NC, Schweiger MR, Krüger U, Frommer G, Fischer B, Kornak U, Flöttmann R, Ardeshirdavani A, Moreau Y, Lewis SE, Haendel M, Smedley D, Horn D, Mundlos S and Robinson PN

    Science translational medicine 2014;6;252;252ra123

  • Improved exome prioritization of disease genes through cross-species phenotype comparison.

    Robinson PN, Köhler S, Oellrich A, Sanger Mouse Genetics Project, Wang K, Mungall CJ, Lewis SE, Washington N, Bauer S, Seelow D, Krawitz P, Gilissen C, Haendel M and Smedley D

    Genome research 2014;24;2;340-8


For questions or comments, please contact Damian Smedley or Jules Jacobsen.

* quick link -