Welcome to Jannovar’s documentation!

Jannovar is a Java-based program and library for the functional annotation of VCF files. The documentation is split into five parts (accessible through the navigation on the left).

Installation & Getting Started
Instructions for the Installation of the program and some examples to get you started.
Jannovar Usage
An overview of how Jannovar works and documentation and examples for the Jannovar sub commands. The original and prime feature of Jannovar predicting molecular impact of variants given a transcriptome model. Further features such as the conversion between HGVS and VCF are also described.
Further Annotation
This part documents the annotation with different databases and compatible modes of inheritance. Also, it quickly describes how to (hard-)filter your VCF files given annotations using bcftools.
Tips & Tricks
Further documentation on Jannovar, information on troubleshooting etc.
Project Information
More information on the project, including the changelog, list of contributing authors, and contribution instructions.

Quick Example

$ java -jar jannovar-0.36.jar \
    download -d hg19/refseq
$ java -jar jannovar-0.36.jar \
    annotate-vcf -d data/hg19_refseq.ser -i IN.vcf.gz -o OUT.vcf.gz



The best place to leave feedback, ask questions, and report bugs is the Jannovar Issue Tracker.