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Documentation Index

This directory contains the repository-facing documentation for CoGA. Use it alongside the in-app user guide at /docs when the application is running.

Start Here

  • Application Scheme
    • Repo-accurate architecture diagrams for the frontend, backend API, storage layers, runtime assets, and import tooling.
  • Storage Architecture
    • CoGA Postgres plus ClickHouse split, schema entrypoints, and migration-status notes.
  • Development and Reset Guide
    • Local setup, Docker versus non-Docker behavior, environment variables, reset steps, and startup troubleshooting.
  • Data Import Guide
    • Canonical import order, CLI versus web upload responsibilities, demo-dataset loading, and supported assay/reference file flows.
  • Database Schema
    • Collection-by-collection schema reference for access control, reference layers, assay data, review state, gene caches, and repeat-expansion data.
  • Security & PHI Posture
    • Access control / RBAC, audit logging (append-only), encryption, and the S3/deployment PHI-scoping checklist, plus the CI gates.
  • Test Overview
    • File-by-file catalogue of the backend (pytest, ~662 tests) and frontend (vitest, 388 tests) suites and the CI gates, with how-to-run and the requirement→test traceability cross-link.
  • Roadmap
    • Current backlog and direction notes.
  • Clinical Traceability, Sign-out & Audit (plan)
    • Proposed design for clinical-grade end-to-end traceability: the annotation/reference version manifest + report footer, per-classification evidence snapshots, annotation-version drift surfacing, an immutable clinical audit trail, and case sign-out with a frozen, versioned report snapshot. Grounded in the current code, with a phased delivery plan.

Also Useful

  • ACMG Classification
    • The semi-automatic ACMG/AMP classifier: the points/scoring model, VUS hot/warm/cold sub-tiers, the mtDNA-specific (McCormick 2020) rule set, and the full pre-check and exclusion rules used to auto-position each criterion.
  • Family Report Template
    • Drafting a clinical report from variants tagged report: variant description, ACMG motivation, gene context and HPO phenotype coupling.
  • Family Member Management
    • How phenotype/carrier/structure edits propagate, what is preserved versus marked stale, and the batch-update flow.
  • Sample-integrity QC
    • Application-aware sample QC: sex concordance, KING relatedness + consanguinity, Mendelian-error rate, and the monogenic-NIPT cfDNA checks (paternity, fetal sex, parent sex, category QC), with thresholds and data sources. It is authored in the frontend so it renders in-app at /docs/reference/sample-qc (linked from the user guide) — viewable in the browser while the repository is private.
  • Haplotype Segregation Analysis
    • The PGT haplotype track: pedigree-aware IBD founder colouring, the raw phased-marker overlay, the four-founder + grey + risk colour code, single-parent (donor) families, the derived embryo classification (affected/carrier/unaffected/uninformative) with recombination/uninformative-marker warnings, and the ROI marker overview + QC signals.
  • Monogenic NIPT Analysis
    • The cfDNA-from-plasma feature (implemented): the 2-sample trio model, fetal-fraction estimation, the eight maternal/fetal VAF categories, quality/artifact filtering, on-target coverage reporting, and the dashboard — built on the small-variant pipeline. Doubles as the design reference.
  • Monogenic NIPT — Fetal Fraction & Classification Algorithm
    • The Phase 3 algorithm reference (implemented): data structures, the category-7 fetal-fraction estimator with external-FF reconciliation, the beta-binomial per-variant classifier and confidence model, the resolvable-vs-not reliability split, edge cases, and the test plan.
  • Demo Quartet Walkthrough
    • File inventory and usage notes for the bundled synthetic family dataset.

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