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Quick Start

This page shows the shortest path for running bff-tools after installation.

If you have not installed the toolkit yet, start with one of these pages:

Genetic Data Interpretation Disclaimer

This tool provides research-based annotations of genetic data from SNP microarray formats (e.g., 23andMe) and VCF (Variant Call Format) files. It is intended for research use only and is not a medical device. It does not provide medical or clinical advice.

  • 🩺 Do not use results for medical decisions. Always consult a qualified healthcare professional.
  • 😰 Results may cause emotional or psychological distress. You may learn about increased risks for serious health conditions.
  • 🔬 Genetic data and interpretations have limitations. Not all variants are covered, and scientific understanding continues to evolve.
  • 🔐 You are responsible for safeguarding your genetic data. Use caution when storing or sharing results; privacy or legal implications may apply.
  • ⚡ Use at your own risk. The authors assume no responsibility for how the results are interpreted or used.

By using this tool, you confirm that you understand and accept these terms.

1. Check the command

bin/bff-tools --help

2. Validate metadata

mkdir bff_out
bin/bff-tools validate -i utils/bff_validator/Beacon-v2-Models_template.xlsx --out-dir bff_out

This validates metadata and writes BFF JSON collections to bff_out.

3. Convert genomic data

VCF input

bin/bff-tools vcf -i testdata/vcf/test_1000G.vcf.gz -p testdata/vcf/param.yaml

SNP-array TSV input

bin/bff-tools tsv -i testdata/tsv/input.txt.gz -p testdata/tsv/param.yaml

Use vcf for VCF or VCF.gz input. Use tsv for SNP-array style TSV or TXT input.

4. Load into MongoDB

Once you have BFF metadata plus genomic variations, load them with:

bin/bff-tools load -p param.yaml

If you want conversion plus loading in one step, use:

bin/bff-tools full -i input.vcf.gz -p param.yaml

Which command do I need?

  • I only want to validate metadata: bff-tools validate
  • I want to convert a VCF: bff-tools vcf
  • I want to convert a SNP-array TSV: bff-tools tsv
  • I already have BFF files and want to ingest them: bff-tools load
  • I want conversion and loading in one run: bff-tools full

Next steps

  • For the full workflow, continue to the tutorial.
  • For installation details, go back to the installation pages.
  • For troubleshooting and edge cases, see the FAQ.