Beacon v2 CBI Tools

Build Beacon v2-ready datasets from metadata and genomic files.

Validate Beacon metadata, convert VCF or SNP-array input into Beacon Friendly Format, and load the resulting collections into MongoDB for Beacon deployments.

Start Tutorial Command Recipes What should I run?

InputXLSX metadataBFF JSONVCF / SNP-array TSV

Runvalidatevcf / tsvload / full

OutputBFF collectionsgenomicVariationsMongoDB / browser files

Open Recipes

Run Commands

Use copy-paste recipes for metadata validation, VCF conversion, SNP-array input, MongoDB loading, and inspection.

View Matrix

Check Supported Data

Confirm which inputs, outputs, commands, and current limits apply before processing a real cohort.

Read Guidance

Review Reproducibility

Understand what schema validation checks, what it cannot prove, and what to keep for reproducibility.

Choose Install Path

Install the Toolkit

Pick Docker, Apptainer, or a non-containerized install depending on your workstation, server, or HPC environment.

Start Tutorial

Prepare Real Data

Follow the end-to-end workflow for metadata validation, genomic conversion, and MongoDB loading.

Open FAQ

Troubleshoot a Run

Use the FAQ when reference genomes, annotation resources, validation warnings, or MongoDB loading fail.