Overview

Beacon v2 data preparation

Turn metadata and genomic files into portable BFF collections.

Build and validate BFF metadata from XLSX, validate existing JSON, convert genomic data, and inspect the result before connecting it to a Beacon implementation.

Start the tutorial Quick start Supported data

Beacon v2 CBI Tools does one job: it prepares data in the Beacon Friendly Format (BFF) for Beacon v2. Its command-line interface is called bff-tools.

Choose a Starting Point

Two minutes

Run the packaged demo

Convert an annotated VCF, validate BFF, and open the standalone browser without external resources.

Complete workflow

Beaconize a dataset

Follow metadata and variants from source files through validation and review.

Quality control

Build trust in the output

Check schema results, provenance, biological assumptions, and reproducibility.

Worked input

Run the GRCh38 example

Recreate and beaconize the included 1000 Genomes chromosome 22 subset.

Help

Resolve a failed run

Find focused answers for workbooks, VCF conversion, annotation, and reports.

Core Commands

Command	Use it for
`bff-tools doctor`	Check installed capabilities and annotation-resource readiness without running a pipeline
`bff-tools demo`	Verify an installation and inspect generated BFF without external annotation resources
`bff-tools validate`	Build and validate BFF metadata from XLSX, or validate existing BFF JSON
`bff-tools vcf`	Convert a VCF or VCF.gz file into BFF `genomicVariations`
`bff-tools tsv`	Convert supported SNP-array text data through VCF into BFF

Raw VCF and SNP-array workflows require the full annotation data to add ANN, dbNSFP, ClinVar, and COSMIC fields before conversion. Annotation is enabled by default. Use --no-annotate only for a VCF that already contains a compatible SnpEff ANN header and annotations.

Research use

The toolkit prepares and validates data structures. It does not establish clinical validity and must not be used by itself for medical decisions.