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-0.11.jar annotate-pos data/hg19_ucsc.ser 'chr1:12345C>A'
[...]
#change effect hgvs_annotation
chr1:12345C>A INTRONIC DDX11L1:uc010nxq.1:c.38+118C>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