The Exomiser2: Annotate and Filter Variants

The Exomiser v2 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 Annovar 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, phenotype data from human and model organisms, and proximity in the interactome to phenotypically similar genes. Predicted pathogenicity data was extracted from the dbNSFP resource. 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.

Read more in our paper: Robinson P, Köhler S, Oellrich A, Sanger Mouse Genetics Project, Wang K, Mungall C, Lewis SE, Washington N, Bauer S, Seelow D, Krawitz P, Gilissen C, Haendel M and Smedley D. Improved exome prioritization of disease genes through cross species phenotype comparison. Genome Research. 2014 Feb;24(2):340-8.

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Required Example single sample file with causative FGFR2 variant for the autosomal dominant Pfeiffer syndrome added to exome of a healthy individual


e.g. Craniosynostosis

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