# 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.