CNAG Biomedical Informatics

Beacon v2 CBI Tools

Turn metadata and genomic files into Beacon Friendly Format.

Use the bff-tools CLI to validate Beacon metadata, annotate and convert VCF or SNP-array input, and inspect portable BFF collections before connecting them to a Beacon implementation.

Quick start Tutorial

Optional run profile

genome: hg38
datasetid: cohort-1
projectdir: cohort-bff
annotate: true
bff2html: true

Metadatavalidated

Variantsannotated

OutputBFF ready

Standalone review

Inspect the generated genomic variations

Run the GRCh38 example

BFF Tools Browser showing an annotated CINECA variant with colored clinical, molecular-effect, type, and filter labels

InputXLSX, JSON, VCF, or SNP-array data

ProcessValidate, annotate, and convert

OutputPortable BFF collections and report

Generated from the annotated CINECA chr22 parity data included with the repository.

Get started

Install and run

Install from PyPI, Docker, Apptainer, or source and produce your first BFF collections.

Workflow

Beaconize a dataset

Take metadata and variants through validation, annotation, conversion, and review.

Annotation

Prepare reference data

Configure the FASTA, SnpEff, dbNSFP, ClinVar, and COSMIC resources used for raw input.

Quality control

Establish trust

Review schema guarantees, biological limits, provenance, and release acceptance checks.