Annotating Positions¶

Sometimes, it is useful to annotate a single position only, for example for quick checks or for debugging purposes. You can do this using the annotate-pos command of Jannovar.

You have to pass a path to a annotation database file and one or more chromosomal change specifiers. Jannovar will then return the effect and the HGVS annotation for each chromosomal change.

# java -jar jannovar-cli-0.16.jar annotate-pos -d data/hg19_ucsc.ser -i 'chr1:12345C>A' 'chr1:12346C>A'
[...]
#change     effect  hgvs_annotation
chr1:12345C>A       CODING_TRANSCRIPT_INTRON_VARIANT        DDX11L1:uc010nxq.1:c.38+118C>A:p.=
chr1:12346C>A       CODING_TRANSCRIPT_INTRON_VARIANT        DDX11L1:uc010nxq.1:c.38+119C>A:p.=

The format for the chromsomal change is as follows:

{CHROMOSOME}:{POSITION}{REF}>{ALT}

CHROMOSOME: name of the chromosome or contig
POSITION: position of the first change base on the chromosome; in the case of insertions the first base after the insertion; the first base on the chromosome has position 1
REF: the reference bases
ALT: the alternative bases