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