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Scout REViewer Service integration

Scout-REViewer-service provides a way to integrate ExpansionHunter REViewer visualisation for short tandem repeats.

Installation

Follow the build and installation instructions on available from the Scout REViewer Service repository.

git clone https://github.com/Clinical-Genomics/Scout-REViewer-service.git

Production ready Docker and Docker compose installation options are available for testing. Modify the .env file to point to your ExpansionHunter case files.

The container, once started, will provide an HTTP interface on a selected port.

Configuration

Point Scout to the Scout-REViewer-service URL host and port by editing the following lines in your scout.config:

# Connection details for Scout REViewer service
# SCOUT_REVIEWER_URL = "http://127.0.0.1:8000/reviewer"

Case configuration files

In your case load configuration file, provide paths to Expansion Hunter individual VCF, realignment bam-let files (not the regular sample full alignment .cram files) and if differing from the defaults given in the SRS configuration, reference genome and Expansion Hunter JSON catalog files. Please see Load Config File for parameter names and details.