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popgenVCF documentation

popgenVCF is an R toolkit and command-line application for reproducible population-genomic analysis of diploid, biallelic SNP VCF files. This wiki is the task-oriented manual. The pkgdown site provides generated API documentation and rendered vignettes.

Development status: 1.0.6 was scientifically approved and released 2026-08-28 (DOI 10.5281/zenodo.22135350, production dossier READY, 15/15 required gates passed). main is now at 1.0.6.9000, an active development build past that release toward the next one (see docs/ROADMAP.md); a green routine CI run on main is not by itself production scientific approval for those unreleased changes -- only a complete candidate dossier for the exact release commit can report READY.

Choose your path

Users

• Getting Started — install, create a configuration, and run a first analysis.
• User Guide — inputs, metadata modes, outputs, and normal workflows.
• Configuration Reference — the main YAML sections and safe defaults.
• Results and Interpretation — how to read QC, PCA, diversity, FST, ancestry, AMOVA, and spatial outputs.
• Deployment and Troubleshooting — Docker, Apptainer, Conda, HPC, and common failures.

Validators and scientific reviewers

• Validation and Scientific Review — validation hierarchy, reviewer packet, manual checklist, approval decision, and return path.
• Scientific validation contract — normative methods and failure policy.

Developers and maintainers

• Developer Guide — repository layout, development environment, tests, modules, documentation, and contribution standards.
• Release and Governance — release gates, evidence, approvals, archival boundaries, and authorization.
• Documentation Map — canonical specifications and where each type of information belongs.

Fastest evaluation path

docker pull ghcr.io/duceppemo/popgenvcf:latest

docker run --rm --user "$(id -u):$(id -g)" \
  -e HOME=/tmp -v "$PWD:/data" \
  ghcr.io/duceppemo/popgenvcf:latest \
  --write-config /data/analysis.yml

Edit analysis.yml, then run:

docker run --rm --user "$(id -u):$(id -g)" \
  -e HOME=/tmp -v "$PWD:/data" \
  ghcr.io/duceppemo/popgenvcf:latest \
  --config /data/analysis.yml

Use an immutable release digest rather than latest for reproducible production work.

Project links

• Repository
• API reference
• Issue tracker
• Roadmap
• Contributing
• Citation