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
- 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.
$ java -jar jannovar-0.33.jar \ download -d hg19/refseq [...] $ java -jar jannovar-0.33.jar \ annotate-vcf -d data/hg19_refseq.ser -i IN.vcf.gz -o OUT.vcf.gz
- annotation of VCF files for functional impact, supporting different transcript databases (RefSeq, ENSEMBL, UCSC)
- annotation with information from dbSNP, ExAC, UK10K, …
- use Sequence Ontology for variant effect annotation
- API Javadoc for the library is here: https://javadoc.io/doc/de.charite.compbio/jannovar-core/0.33/.
- … and more
The best place to leave feedback, ask questions, and report bugs is the Jannovar Issue Tracker.
The friendly people at javadoc.io host our API documentation: