The list of genes associated with given disease is then enriched by the script stored
stored in the `extend_network` directory.
#### **enrich_maps.R** Script for map and pathway enrichment
Should be run as `Rscript --vanilla enrich_maps.R <input_filename> <config_file>`
-`input_filename` should contain list of genes as HGNC symbols, one entry per line. Default is "input.txt" in the script folder.
-`config_file` contains the list of map instances and pathways to enrich. Default is "config.txt" in the script folder.
The script uses "config.txt" file, containing the list of minerva instances and
pathways to query for enriched areas.
It provides output with the list of enriched map areas and pathways.
Statistical tests used for maps and pathways are different.
## 3. Filter variants by allele frequency
#### Ensembl
The script [vepAllInOne.py](bh19-rare-diseases/associations/vepmining) retrives information about [allele frequencies](https://en.wikipedia.org/wiki/Allele\_frequency) in several populations available in the [Ensembl](http://www.ensembl.org/index.html) databse. This is done throug [this endpoint](https://rest.ensembl.org/documentation/info/vep\_id\_post) of the Ensembl API.