Functional variant file annotation in Java. Jannovar provides a program for the annotation of VCF files and also exposes its functionality through a library API.
Jannovar is licenced under the BSD2 license.
More information is available in the Jannovar manual.
Download binary files of the current release from our GitHub release page.
After extracting the ZIP file, you can call Jannovar as follows.
Download the UCSC transcripts for hg19:
# java -jar jannovar-cli-0.11.jar download hg19/ucsc
[...]
Annotate the example file small.vcf:
# java -jar jannovar-cli-0.11.jar annotate data/hg19_ucsc.ser examples/small.vcf
[...]
Inspect the resulting annotated file:
# less small.jv.vcf
Also see the Quickstart section in the Jannovar manual.