Quickstart¶
This short How-To guides you from downloading the Jannovar program to annotating a VCF file in 5 steps.
Download the current stable release from our GitHub project by clicking here.
Extract the ZIP archive.
- you should find file called
jannovar-cli-0.16.jar
in the ZIP - you should also find a file
small.vcf
file in the folderexamples
- you should find file called
Download the RefSeq transcript database for the release hg19/GRCh37.
Note
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-0.16.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.Annotate the file
small.vcf
from theexamples
directory.# java -jar jannovar-cli-0.16.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 readexamples/small.vcf
file. Each contained variant in this file will be annotated with anEFFECT
and anHGVS
field in theVCF
info column. TheEFFECT
field contains an effect, e.g.,SYNONYMOUS
and theHGVS
field contains a HGVS representation of the variant. The result will be written out tosmall.jv.vcf
.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 here.
- HGVS Mutation Nomenclature.
- is mainainted by the Human Genome Variation Society and the nomenclature can be found here.