A Java library for Exome Annotation

Transcript-based annotation and pedigree analysis are two basic steps in the computational analysis of whole-exome sequencing experiments in disease-gene discovery projects or diagnostics. Jannovar is a stand-alone Java application as well as a Java library designed to be used in larger software frameworks for exome analysis. Jannovar uses an interval tree to identify all transcripts affected by a given variant, and provides HGVS-compliant annotations for both for variants affecting coding sequences and splice junctions as well as UTR sequences and non-coding RNA transcripts. Jannovar can also perform family-based pedigree analysis with VCF files with data from members of a family segregating a Mendelian disorder. Using a desktop computer, Jannovar requires a few seconds to annotate a typical VCF file with exome data.


For convenience, we provide a compiled version of the Jannovar executable. The latest version of jannovar is always available at the project github repository. See the instructions in the online manual for information about how to use Jannovar.


Downloading the source code

Developers can download the entire source code for the Jannovar project in the form of a maven repository from https://github.com/charite/jannovar.

License issues

Jannovar is distributed under a BSD2 license.