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-.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