Annotating PositionsΒΆ

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-0.35-SNAPSHOT.jar annotate-pos \
-d data/hg19_refseq.ser -c 'chr1:12345C>A' -c 'chr1:12346C>A'
[...]
#change     effect  hgvs_annotation
chr1:12345C>A   NON_CODING_TRANSCRIPT_INTRON_VARIANT    DDX11L1:NR_046018.2:n.354+118C>A:
chr1:12346C>A   NON_CODING_TRANSCRIPT_INTRON_VARIANT    DDX11L1:NR_046018.2:n.354+119C>A:

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