This short How-To guides you from downloading the Jannovar program to annotating a VCF file in 4 steps.

  1. Download the current stable release from our GitHub project by clicking here .

  2. Extract the ZIP archive.

    • you should find file called jannovar-cli-0.35-SNAPSHOT.jar in the ZIP
    • you should also find a file small.vcf file in the folder examples
  3. Download the RefSeq transcript database for the release hg19/GRCh37.


    If you are behind a proxy then you have to pass its path to the --proxy option, e.g., --proxy http://proxy.example.com:8080. See the section Proxy Settings for more information.

    $ java -jar jannovar-cli-0.35-SNAPSHOT.jar download -d hg19/refseq

    This will create the file data/hg19_refseq.ser which is a self-contained transcript database and can be used for functional annotation.

  4. Annotate the file small.vcf from the examples directory.

    $ java -jar jannovar-cli-0.35-SNAPSHOT.jar annotate -d data/hg19_refseq.ser -i examples/small.vcf

    Jannovar will now load the transcript database from data/hg19_refseq.ser and then read examples/small.vcf file. Each contained variant in this file will be annotated with an EFFECT and an HGVS field in the VCF info column. The EFFECT field contains an effect, e.g., SYNONYMOUS and the HGVS field contains a HGVS representation of the variant. The result will be written out to small.jv.vcf.


    The variant effect codes in the output and their mapping to sequence ontology is described in the Jannovar API documentation.

    The following excerpt shows the first three variants of the small.vcf file with their effect and HGVS annotation.

    1 866511  rs60722469      C       CCCCT   258.62  PASS    EFFECT=INTRONIC;HGVS=SAMD11:NM_152486.2:c.305+42_305+43insCCCT  GT:AD:DP:GQ:PL  1/1:6,5:11:14.79:300,15,0
    1 879317  rs7523549       C       T       150.77  PASS    EFFECT=MISSENSE;HGVS=SAMD11:XM_005244727.1:exon9:c.799C>T:p.Arg267Cys   GT:AD:DP:GQ:PL  0/1:14,7:21:99:181,0,367
    1 879482  .       G       C       484.52  PASS    EFFECT=MISSENSE;HGVS=SAMD11:XM_005244727.1:exon9:c.964G>C:p.Asp322His   GT:AD:DP:GQ:PL  0/1:28,20:48:99:515,0,794

Next Steps

Of course, you can follow the other manual chapters and get more extensive information on Jannovar. In addition, here are some external links that can help you in your understanding:

Current VCF Specification
can be found in the hts-specs project on GitHub.
HGVS Mutation Nomenclature.
is mainainted by the Human Genome Variation Society and the nomenclature can be found in the Sequence Variant Nomenclature.