P5a: QC — control metrics, thresholds, status, contamination, relatedness, locus summary

- qc/controls: canonical control names (QC-002), bkg/offset (QC-003), 13 genotyping metrics (QC-004/005),
  missing/zero-divisor handling (QC-007/008); controls_raw.tsv / controls_qc.tsv (QC-009/011) incl. compat CSVs
- qc/thresholds + profiles: YAML schema, validation codes, precedence, shipped profiles, auto (QC-020..025)
- qc/status: functional PASS/FAIL/NA, control CLEAR/FLAGGED, flags (QC-030..033)
- qc/contamination: BAF regression; bit-compatible with gtc2vcf BAFregress (36/36, K-017), exact mode too
- qc/relatedness: KING-robust, duplicates, Mendelian errors, pedigree from sheet (IN-018)
- qc/locus_summary: OUT-072, bit-identical to BeadArrayFiles except ChiTest (K-018)
- qc/suggest: suggest-thresholds (QC-026)
- pipeline/qc: disk-backed cohort store; CLI qc controls|samples|contamination|relatedness|loci|suggest-thresholds
- genotype: control tables (OUT-070), het_rate, QC columns, cohort QC
- tests: unit + oracle (BAFregress plugin, BeadArrayFiles locus summary)

docs/validation/P5.md

@@ -0,0 +1,22 @@
+# Phase P5 validation — QC
+
+Status: **part 1 (local, GSA v4 PGx demo, 36 samples) passed**; part 2 (1000 Genomes Omni2.5, 2141 samples, cloud) pending.
+
+## Part 1 — local, against open-source references (`tests/oracle/test_p5_qc.py`)
+
+| Check | Reference | Result |
+|---|---|---|
+| BAF-regression contamination, 36 samples, all 683 054 loci as sites | gtc2vcf `bcftools +BAFregress` (MIT), built by `scripts/make_oracle_gtcs.sh` | 36/36 identical at the plugin's printed precision (`%.4f`), homozygous-site counts identical (K-017: float threshold 0.1f and klib quickselect median reproduced) |
+| Locus summary, 683 054 loci | BeadArrayFiles `examples/locus_summary.py` (BSD-2), `scripts/make_oracle_qc.sh` | every column bit-identical except ChiTest_P100 (≤ 3.6e-15 relative, K-018) |
+| Control metrics | QC-004 formulas | unit tests with hand-computed values; GSA demo values plausible (staining, extension, NP > 5; hyb > 1) |
+| Thresholds / profiles / status / flags | QC-020 … QC-033 | unit tests for every QC-021 error code, precedence, aliases, profiles, both status axes |
+| KING-robust kinship, Mendelian errors | Manichaikul 2010 | simulated trio: duplicate φ = 0.50, parent–child φ ≈ 0.25, unrelated ≈ 0, 0 Mendelian errors in the true trio |
+| End to end | `simurg qc controls`, `simurg genotype` with QC | control tables identical between the two paths; QC columns filled |
+
+GSA demo observations: all 36 samples PASS (autosomal call rate ≥ 0.997, LogR dev 0.13–0.17), control status CLEAR;
+contamination 0.0012–0.0040; replicate pairs (φ ≈ 0.50) and first-degree relatives (φ ≈ 0.25) are present (K-019).
+
+## Part 2 — cohort scale (pending)
+
+1000 Genomes Omni2.5, 2141 samples: relatedness and Mendelian errors against the 1000G pedigree (trios), sex against the
+pedigree, contamination and control-metric distributions, runtime/memory of the disk-backed cohort store.