fdlk / vkgl

vkgl

Variant annotator for vkgl variant sharing. Consists of two parts:

hgvs translator

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'

file processing pipeline

Spring Boot application that uses Apache Camel to read input file from src/test/resources 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