> 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/organization-databases.md).
# Organization databases
**Organization databases (DBs)** provide custom [annotation](/emedgene/emedgene-analyze-manual/tertiary-analysis-pipeline/annotations-from-organization-databases.md) sources for case analysis. During case analysis, Emedgene applies these annotations to variants, so you can filter and review variants against your own data.
Organization databases are grouped by what they store:
* [**Variant databases**](#variant-databases): Store variants and their associated values, such as allele frequencies or curated classifications.
* [**Region databases**](#region-databases): Store genomic regions.
***
## Variant databases
Variant databases are registered from a VCF file. A variant in a case is annotated when it matches an entry in the database.
Historic, noise, and curated databases are variant databases
### Historic database
A historic database provides private population frequencies from cases processed in your organization's **Emedgene** account.
A historic database typically includes all unique cases at the time of creation but can be tailored to include only specific cases.
Use variant frequencies in a historic database to [filter out](/emedgene/emedgene-analyze-manual/reviewing_a_case/analysis-tools-tab-beta-v100.39.0+/filters_presets_panel/filters/quick-filters/polymorphism_filters.md#maximum-allele-frequency-in-organizational-databases) variants that are common in the population of interest.
### Noise database
A noise database identifies recurring artifacts associated with a sequencing technique, platform, or analysis pipeline.
Noise databases commonly use samples from unaffected individuals. If only affected sample data are available, use caution when filtering rare variants to avoid excluding variants of interest; the database still might be useful for filtering out high-frequency artifacts.
Sample size recommendations:
* Use at least 100 samples to filter variants with an allele frequency greater than 5%.
* Use at least 350 samples to filter variants with an allele frequency greater than 1%.
You can maintain multiple noise databases for different assays and calling methodologies.
Use variant frequencies in a noise database to [filter out](/emedgene/emedgene-analyze-manual/reviewing_a_case/analysis-tools-tab-beta-v100.39.0+/filters_presets_panel/filters/quick-filters/polymorphism_filters.md#maximum-allele-frequency-in-organizational-databases) recurring technical artifacts.
### Curated database
{% hint style="warning" %}
A curated organization database is separate from the dynamic [**Curate**](/emedgene/emedgene-curate-manual/curate_overview.md) database.
{% endhint %}
A curated database is a static variant database that serves as a reference of previously curated variants.
Implemented upon request.
Use [known-variant filters](/emedgene/emedgene-analyze-manual/reviewing_a_case/analysis-tools-tab-beta-v100.39.0+/filters_presets_panel/filters/quick-filters/variant_effect_filters.md#advanced) to filter variants by their presence in a curated database.
### Variant database types
#### By origin
* **Internal DBs:** [Built from cases](/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) processed in your organization’s **Emedgene** account. Internal databases can be historic or noise databases.
* **External DBs:** [Created from other sources](/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), such as cases analyzed with other software, research cohorts, legacy data, or public data sets.
#### By included variant types
* **SNV DBs:** Store single nucleotide variants (SNVs).
* **CNV DBs:** Store copy number variants (CNVs), insertions >50bp (INS), short tandem repeats (STRs), and regions of homozygosity (ROH).
***
## Region databases
Region databases are registered from an organization kit BED file that defines genomic regions. A variant in a case is annotated when its coordinates overlap a region in that file.
Custom BED annotation is the only region database type.
### Custom BED annotation database
A custom BED annotation database uses an organization kit BED file to define custom genomic regions. **Emedgene** compares variant coordinates with the regions in the BED file and applies the corresponding region annotation to overlapping variants.
Custom BED annotation filters can be used in presets to filter variants by these region annotations. To include these filters in your presets, reach out to your Illumina representative.
From v100.41 onwards, custom BED annotation databases are configurable in [**Organization DB management**](/emedgene/emedgene-analyze-manual/settings/organization_settings_-330+/workbench-and-pipeline/organization-db-management.md) without the need to involve Illumina Support. The database files come from [**BED files**](/emedgene/emedgene-analyze-manual/settings/organization_settings_-330+/kit-management/bed-files.md) under **Kit management**.
{% hint style="info" %}
Custom BED Annotation databases configured before v100.41 remain available in the **Organization DB Management** table. You do not need to recreate them.
{% endhint %}
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