Variant annotator for vkgl variant sharing. Consists of two parts:
Uses the biocommons/hgvs
library to convert hgvs to vcf.
To start the translator service:
> cd docker
> docker-compose up
To see it in action, post an array of hgvs strings to the h2v endpoint:
curl -H 'Content-Type: application/json' -d '["NM_000088.3:c.589G>T", "NC_000017.10:g.48275363C>A"]' 'http://localhost:1234/h2v?keep_left_anchor=False'
Spring Boot application that uses
Apache Camel to read input files from src/test/inbox
and annotate the lines with vcf info retrieved from the hgvs annotator.
Results will be stored in results dir once finished. Results with an error message will be routed to error file.
Requires JDK 8. To run the pipeline:
> mvn clean spring-boot:run