> For the complete documentation index, see [llms.txt](https://help.bioinsight.illumina.com/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://help.bioinsight.illumina.com/emedgene/emedgene-analyze-manual/settings/organization_settings_-330+/workbench-and-pipeline/organization-db-management/configuring-an-organization-database.md).

# Configuring an organization database

How you configure an organization database depends on whether it uses a VCF file (variant databases) or an organization kit BED file (region databases).

Configuring a database requires [permissions](/emedgene/emedgene-analyze-manual/settings/user_roles/iam-scopes-emedgene-roles.md).

## Configure a historic, noise, or curated database

{% stepper %}
{% step %}
Obtain the database VCF file.

* Request that Illumina Support [provision an internal database VCF file](/emedgene/emedgene-analyze-manual/settings/organization_settings_-330+/workbench-and-pipeline/organization-db-management/configuring-an-organization-database/creating-a-variant-database-vcf-file/creating-an-internal-variant-database-vcf-file.md) from your organization's cases, based on the requirements you supply.
* Alternatively, [create an external database VCF file](/emedgene/emedgene-analyze-manual/settings/organization_settings_-330+/workbench-and-pipeline/organization-db-management/configuring-an-organization-database/creating-a-variant-database-vcf-file/creating-an-external-variant-database-vcf-file.md) and provide it to Illumina Support for upload.
  {% endstep %}

{% step %}
[Register the database](/emedgene/emedgene-analyze-manual/settings/organization_settings_-330+/workbench-and-pipeline/organization-db-management/configuring-an-organization-database/registering-a-database.md): Fill database details and select the VCF file from your organization's bucket.

Once registered, the database appears in the organization databases list in the [**Organization DB Management** **card**](/emedgene/emedgene-analyze-manual/settings/organization_settings_-330+/workbench-and-pipeline/organization-db-management.md).
{% endstep %}

{% step %}
[Modify the database settings](/emedgene/emedgene-analyze-manual/settings/organization_settings_-330+/workbench-and-pipeline/organization-db-management/configuring-an-organization-database/modifying-database-settings.md):

* Enable or disable its use in [variant annotation](/emedgene/emedgene-analyze-manual/tertiary-analysis-pipeline/annotations-from-organization-databases.md).
* Enable or disable allele frequency usage by **AI Shortlist** for variant prioritization.
* Select a different VCF file.
  {% endstep %}
  {% endstepper %}

## Configure a custom BED annotation database

Starting with v100.41, you can configure a custom BED annotation database without Illumina Support.

{% hint style="info" %}
Custom BED Annotation databases configured before v100.41 in the organization settings file remain valid, appear in the **Organization DB Management** table, and do not need to be recreated.
{% endhint %}

{% stepper %}
{% step %}
In **Organization Settings** > **Kit management** > [**BED files**](/emedgene/emedgene-analyze-manual/settings/organization_settings_-330+/kit-management/bed-files.md), upload the BED file that defines the custom genomic regions.
{% endstep %}

{% step %}
[Register the database](/emedgene/emedgene-analyze-manual/settings/organization_settings_-330+/workbench-and-pipeline/organization-db-management/configuring-an-organization-database/registering-a-database.md): Fill database details and select the organization kit BED file.
{% endstep %}

{% step %}
[Modify the database settings](/emedgene/emedgene-analyze-manual/settings/organization_settings_-330+/workbench-and-pipeline/organization-db-management/configuring-an-organization-database/modifying-database-settings.md):

* Enable or disable its use in [variant annotation](/emedgene/emedgene-analyze-manual/tertiary-analysis-pipeline/annotations-from-organization-databases.md).
* Select a different BED file.
  {% endstep %}
  {% endstepper %}

## Learn more

<table data-view="cards"><thead><tr><th></th><th></th><th></th></tr></thead><tbody><tr><td><strong>Creating a variant database VCF file</strong></td><td>Prepare an internal or external VCF file for a historic, noise, or curated database.</td><td><i class="fa-arrow-up-right-from-square">:arrow-up-right-from-square:</i> <a href="/emedgene/emedgene-analyze-manual/settings/organization_settings_-330+/workbench-and-pipeline/organization-db-management/configuring-an-organization-database/creating-a-variant-database-vcf-file.md">Learn more</a></td></tr><tr><td><strong>Registering a database</strong></td><td>Add a database in the <strong>Organization DB Management card</strong> and select its file.</td><td><i class="fa-arrow-up-right-from-square">:arrow-up-right-from-square:</i> <a href="/emedgene/emedgene-analyze-manual/settings/organization_settings_-330+/workbench-and-pipeline/organization-db-management/configuring-an-organization-database/registering-a-database.md">Learn more</a></td></tr><tr><td><strong>Modifying database settings</strong></td><td>Activate a database, change its file, and control its use by <strong>AI Shortlist</strong>.</td><td><i class="fa-arrow-up-right-from-square">:arrow-up-right-from-square:</i> <a href="/emedgene/emedgene-analyze-manual/settings/organization_settings_-330+/workbench-and-pipeline/organization-db-management/configuring-an-organization-database/modifying-database-settings.md">Learn more</a></td></tr><tr><td><strong>Organization DB management</strong></td><td>Manage organization databases: configure, define settings, review details, and search.</td><td><i class="fa-arrow-up-right-from-square">:arrow-up-right-from-square:</i> <a href="/emedgene/emedgene-analyze-manual/settings/organization_settings_-330+/workbench-and-pipeline/organization-db-management.md">Learn more</a></td></tr></tbody></table>


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