Annotate snp list with amino acids.
- min. Java 11
Please download the file genepi-annotate.jar from the latest release.
java -jar genepi-annotate.jar annotate --input <string> --mutation <string> --position <string> --output <string> --columnmut <string> --columnwt <string> --reference <string> --maplocus <string>
| Option | Description |
|---|---|
--input <string> |
Input csv file |
--mutation <string> |
Mutation column in input file |
--position <string> |
Position column in input file |
| Option | Description |
|---|---|
--output <string> |
Output csv file |
--columnmut <string> |
New column for wt aas in output file |
--columnwt <string> |
New column for wildtype aas in output file |
| Option | Description |
|---|---|
--maplocus <string> |
MapLocus filename |
--reference <string> |
Reference fasta file |
java -jar genepi-annotate.jar annotate --input test-input.txt --position POS --mutation MUT --output test-output.txt --columnwt wt_aas --columnmut mut_aas --reference reference.fasta --maplocus maplocus.txt
The MapLocus presents a tabular representation of genomic loci along with pertinent details regarding their positions, characteristics, and coding attributes. It delineates various genomic elements such as introns, exons, splice sites, and their respective positions within a genomic sequence.
In brief, it assigns a freely definable denominator (column MapLocus) to portions of the reference sequence, as specified by the position columns.
Also a shorthand denominator and a description of the defined region can be added in the respective columns. The columns coding and translated define whether our annotation tool should translate the respective sequence sequence.
The column ReadingFrame then specifies whether the translation, respectively reading frame starts at base 1 2 or 3 of the respective feature.
An example can be found here.
This software was developed at the Institute of Genetic Epidemiology, Medical University of Innsbruck
genepi-annotate is MIT Licensed.