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.
- $ java -jar jannovar-.jar \
download -d hg19/refseq
[...] $ java -jar jannovar-.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: .
- ... 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:
- jannovar-core
- jannovar-hgvs
- jannovar-htsjdk
- jannovar-vardbs
quickstart install
download annotate_vcf annotate_pos annotate_csv hgvs_to_vcf ped_filters jannovar_lib
annotate_vcf_databases inheritance filter
memory proxy datasource faq
contributing authors history license