kemalandClaude Opus 5.5
0c004f6398
- 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) Co-Authored-By: Claude Opus 5.5 <[email protected]> Claude-Session: https://claude.ai/code/session_01814GKVzZVL3FuF3DeiZXhv
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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.