The central hub forgenomic databases
Access, query, and integrate curated genomic datasets directly into your bioinformatics pipelines. Unified schemas, instant access, zero maintenance.
What is GeneBe Hub?
GeneBe Hub is an open repository for genetic variant databases. Like PyPI for Python packages or Docker Hub for container images, it serves as a repository for annotations. You can add your own databases — private or public — or use existing ones prepared by other users.
How to use databases?
Databases can be used to annotate your VCF files with the GeneBeClient. Additional tools, including Python Pandas integration, will be released soon.
Featured Databases
High-quality, curated datasets ready for immediate use.
ClinVar
A freely accessible, public archive of reports of the relationships among human variations and phenotypes, with supporting evidence. Evergreen.
gnomAD
The Genome Aggregation Database. Spanning diverse global populations, it provides allele frequencies for interpreting variants.
SpliceAI
State of the art splicing effect predictor, estimating how likely a variant is to disrupt normal splicing.
dbSNP
A collection of single nucleotide polymorphisms (SNPs) and other short genetic variations.
Why GeneBe Hub?
GeneBe Hub is designed to make genetic variant annotations easier and more accessible. It's a place where genetic databases are:
Easy to find
A single place for all the databases you need.
Easy to parse
A standardized format — no more dealing with custom TSV files with unusual headers.
Easy to use
If your variants are in VCF format, annotation is as simple as running one command.
Easy to keep evergreen
A new version of a database is available? Just pull the latest version and annotate again.
Quickstart Guide
Integrate Genebe Hub into your workflow in minutes with the Java GeneBeClient — no separate account setup required for public databases.
Download the CLI
Get the newest GeneBeClient from GitHub. Requires Java 21 or newer.
Pull & Annotate
Pull a database once, then annotate any VCF file with it, offline.
$ java -jar GeneBeClient.jar annotation pull --id @genebe/clinvar
$ java -jar GeneBeClient.jar vcf annotate --input-vcf input.vcf --output-vcf output.vcf --annotations "@genebe/clinvar"
Need Help?
Explore our guides and documentation to get started.