Adding HGMD professional to a local install

[lwin2022]

Hi, my group has access to HGMD professional and we have a local copy of the HGMD pro database as a vcf. We also have a local install of seqr. How would I go about changing the HGMD annotations in this local install to HGMD professional? Would I need to replace the combined_reference_data_grch38.ht or can I add it as an additional annotation? Will I need to convert the vcf to a hail table?
I'm not sure how to proceed. Any information would be great.
Thanks

[hanars]

Hello, can you clarify whether you are running the elasticsearch backend with a docker compose installation or the hail-based backend with a helm installation? The process is a bit different depending

[lwin2022]

I'm using the elasticsearch backend with a docker compose installation

[hanars]

As a preface, including HGMD in local installations is not well supported so there is no easy and straightforward way to add this. Below are the steps you will need to do in order to include HGMD.

HGMD is added from a standalone hail table and does not need to be added to the combined reference data. In order to add HGMD data, you will need to construct a hail table with the data. This is not well supported unfortunately, but here is a script you can adapt locally to import your HGMD VCF and output a hail table: https://github.com/broadinstitute/seqr-loading-pipelines/blob/main/v03_pipeline/lib/reference_datasets/hgmd.py
You will want to add this hail table to the same mounted directory you use for all the other reference data - I would recommend using the file path /seqr-reference-data/GRCh38/hgmd.GRCh38.ht

When loading, you will not be able to use the load_data.sh helper script directly, you will need to copy the command out of it and modify it to add the hgmd path. You can find the command from the script here: https://github.com/broadinstitute/seqr-loading-pipelines/blob/main/docker/bin/load_data.sh#L25
You will need to add the argument --hgmd-ht-path "/seqr-reference-data/GRCh38/hgmd.GRCh38.ht"

Once you load data using the --hgmd-ht-path flag you will also need to enable HGMD for that project in seqr. This can be done through the Django admin (/admin/seqr/project/) - select the project with HGMD data, check the "Enable hgmd" checkbox on the "Change project" page, and the click save