Java framework and program for annotating VCF files with gene/transcript-based annotations

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Jannovar: A Java library and program for Exome/Genome Annotation

Transcript-based annotation and pedigree analysis are two basic steps in the computational analysis of whole-exome/genome 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/genome 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/genome data.

Jannovar Documentation

For usage information, installation and other help please visit our Jannovar Manual .

You can find an up-to-date link to the Jannovar API Javadoc (jannovar-core) here.


Refer to the Quickstart or Installation section of the manual.


Report bugs on GitHub issue tracker

If you are reporting a bug, please include:

  • Your operating system name and version.
  • Any details about your local setup that might be helpful in troubleshooting.
  • Detailed steps to reproduce the bug.

Software using Jannovar

Jannovar can be used from the command line to annotate VCF files, but it is also a complete Java programming library that can be used within larger applications. For instance, the Exomiser is a Web server that can be used to prioritise candidate genes in exome sequencing studies. PhenIX is a Web server that provides a ranked list of candidate genes in diagnostic exome or gene panel sequencing. Phenome Central is used for genomic matchmaking.


Jannovar is distributed under a 3-clause BSD2 license.


J├Ąger, Marten, et al. "Jannovar: A Java Library for Exome Annotation." Human mutation 35.5 (2014): 548-555.