The Exomiser is a Java program that functionally annotates variants from whole-exome sequencing data in VCF 4 format. The functional annotation is performed with Jannovar and uses UCSC KnownGene transcript definitions and hg19 genomic coordinates.

Variants are prioritized 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.