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HTS Bioinf - Update external reference data


This procedure explains how to update the external reference data used by the gene panel builder service.


A bioinformatician from GDx is responsible for performing these tasks.

The gene panel builder service

An instance of the gene panel builder service database must be running on the computer the update is to be performed on.

Prior to update

Notify the lab doctors ( that you intend to upgrade reference data.


# make sure that the gene panels repository is up to date with the remote
git -C genepanel-store checkout '<latest-release-tag>'
# open a Bash shell in a gene panel builder Docker container
docker compose --project-directory config exec -it gpbuilder bash

Hereafter, we will assume that the user is inside the Docker container running the GPB backend.

Before performing the update, make sure that a valid OMIM API key is stored in the OMIM_API_KEY env variable (echo $OMIM_API_KEY).

Update all external data with gpb update --diff all-external.

Note: To create tsv-files showing the effects of an update without committing to the database (useful for testing), run gpb --dry-run update --diff all-external.

Create drafts

Once the update is successfully completed, gene names, inheritance, transcripts and PanelApp panels/gene content may have changed. To avoid releasing gene panels with the same version, but different configuration, run the command:

gpb diff --create-drafts --skip-draft-if-no-gene-changes /current-panels

This command will bump versions of all panels with content differing from that of their exported counterparts.

Take note of the panels (if any) listed with the warning These panels remain at draft stage after version bumping and require expert review.

Create diff

Create a diff of all active database panels against panels in production:

gpb diff -o ${LOGS_DIR}/gpb-diff-$(date '+%Y-%m-%d).tsv /current-panels

Notify ELL

Send the generated diffs (gpb-diff-YYYY-MM-DD.tsv and gpb-diff-YYYY-MM-DD.summary.tsv) to the lab doctors. Notify them of which panels (if any) have no submitted version after updating - these are the panels that need to be manually inspected and resubmitted to be part of the next panel release.