Core Toolchain

These entry points are part of the main bff-tools data-preparation workflow.

User-Facing Entrypoints

Entrypoint	Language	Purpose
bin/bff-tools		Main command-line interface for vcf, tsv, validate, load, and full workflows
utils/bff_validator/bff-validator		Validator used by bff-tools validate for Beacon metadata in XLSX or JSON form

Pipeline Helpers

These helpers are normally called by bin/bff-tools, not by end users directly.

Helper	Language	Purpose
pipeline/internal/partial/run_tsv2vcf.sh		Converts SNP-array TSV/TXT input into a VCF-like intermediate
pipeline/internal/partial/run_vcf2bff.sh		Runs VCF normalization, annotation, and BFF conversion
pipeline/internal/partial/run_bff2html.sh		Builds static browser-oriented output
pipeline/internal/partial/run_bff2mongodb.sh		Loads BFF collections into MongoDB
pipeline/internal/complete/vcf2bff.pl		Converts annotated VCF records into BFF genomicVariations
pipeline/internal/complete/bff2json.pl		Prepares JSON data for browser output
pipeline/internal/complete/bff2html.pl		Generates static HTML browser output

Practical Notes

• bff-tools validate delegates validation to utils/bff_validator/bff-validator.
• bff-tools vcf, bff-tools tsv, and bff-tools full use the shell wrappers under pipeline/internal/partial/.
• The Perl scripts under pipeline/internal/complete/ contain the conversion logic used by those wrappers.