SEPIA — evaluation & QC plan (retired — now merged into `plan.md`)
SEPIA — evaluation & QC plan (retired — now merged into plan.md)
This file has been retired. Its 10 reviewer-driven, unit-test-style QC checks are now tracked as first-class items
Q1–Q10inside the single master plan,plan.md§4, interleaved with the fixes/builds they verify (eachQitem sits in the phase whose work it proves, with full acceptance criteria, subtasks, deliverable, and communication artifact). There is no longer a separate QC to-do list — track everything inplan.md.
Where each check went (same two guiding principles as before — provenance before analysis, and reproduce known truth first / positive controls):
| Was (evaluation item) | Now (plan.md) | Phase |
|---|---|---|
| 1. Data-provenance manifest + checksums | Q1 | 0 |
| 2. Genome-build & contig-naming lint (tracer SNPs) | Q2 | 1 |
| 3. Positive control — reproduce SGDP WG-PCA | Q3 | 2 |
| 4. Allele & annotation harmonization | Q4 | 1 |
| 5. PCA / projection non-degeneracy | Q5 | 2 |
| 6. Per-sample coverage expectations | Q6 | 2 |
| 7. Sample identity, sex & contamination | Q7 | 3 |
| 8. aDNA authenticity / damage handling | Q8 | 3 |
| 9. Cross-validation vs published + orthogonal predictor | Q9 | 4 |
| 10. Reproducibility infra (versions, seeds, DAG, CI) | Q10 (+ Q10a in Phase 0) | 5 |
See plan.md for the live, checkbox-tracked versions. Dated history is in changelog.md.