beacon2-cbi-tools 2.0.13

Validate and convert data to Beacon v2 Beacon Friendly Format

Beacon v2 CBI Tools

Beacon v2 CBI Tools prepares portable Beacon Friendly Format (BFF) data for Beacon v2. Its command-line interface is called bff-tools. It validates phenotypic and clinical metadata, converts VCF or SNP-array TSV input into BFF genomicVariations, and can generate a standalone browser report.

Beacon v2 CBI Tools is the actively developed continuation of the original beacon2-ri-tools codebase, now developed at CNAG Biomedical Informatics by its original developer.

The two historical image badges preserve the download record of earlier distributions; those images are deprecated for new installations.

The output remains independent of a particular Beacon server or database. For serving, consider the Beacon v2 Production Implementation or bycon.

Read the documentation for installation options, the quick start, the end-to-end tutorial, CLI reference, annotation resources, and troubleshooting.

Install

python3 -m pip install beacon2-cbi-tools

Python 3.10 through 3.14 is supported. Docker, Apptainer, and source/HPC instructions are available in the installation guide.

Check the installation and run the packaged example without downloading annotation databases:

bff-tools doctor
bff-tools demo

Data flow

Roadmap

• Follow Beacon v2 developments, including VRS alignment.
• Move to Beacon v3 once the specification is finalized.

Citation

If you use these tools in published work, please cite:

Rueda M, Ariosa R. "Beacon v2 Reference Implementation: a toolkit to enable federated sharing of genomic and phenotypic data." Bioinformatics, btac568. https://doi.org/10.1093/bioinformatics/btac568

License

Written by Manuel Rueda, PhD, at CNAG Biomedical Informatics. Licensed under the GNU General Public License v3.0 or later; see LICENSE.