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P5a: QC — control metrics, thresholds, status, contamination, relatedness, locus summary
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- 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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kemalandClaude Opus 5.5 committed 2026-09-28 08:35:10 +01:00
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docs/known_unknowns.md
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@@ -4,6 +4,9 @@ Plan §20 lists the open questions; this file records what the implementation ha
| ID | Date | Topic | Finding | Status |
|---|---|---|---|---|
| K-019 | 2026-09-28 | GSA demo relatedness | The 36-sample GSA v4 PGx demo set contains duplicate/replicate pairs (KING φ ≈ 0.50, concordance ≥ 0.9999) and first-degree relatives (φ ≈ 0.25); without a pedigree they are flagged `duplicate_of:`/`unexpected_relatedness` as designed. Useful as a small relatedness fixture. | documented |
| K-018 | 2026-09-28 | Locus-summary ChiTest_P100 | Against BeadArrayFiles `locus_summary.py` all columns are bit-identical on 36 GSA samples (683 054 loci) except ChiTest_P100, which differs by ≤ 3.6e-15 relative in ~15 % of loci: scipy 1.18's `ndtr` matches neither libm nor a cephes erf/erfc port bit-for-bit. Accepted (p-value). | accepted |
| K-017 | 2026-09-28 | BAF-regression median quirk | gtc2vcf `BAFregress` (1) compares AF with the threshold as a float (0.1f), and (2) for an even number of AA/BB calls averages the quickselect result with whatever element klib `ks_ksmall` leaves just below it, not the lower middle value. Both reproduced (`--median reference`, default): 36/36 GSA samples identical to the plugin at its printed precision; `--median exact` gives the true median. SimurgArray uses autosomal sites only in pipelines; the plugin uses every VCF record. | resolved |
| K-016 | 2026-09-28 | Sex rule of AutoCall 1.6.2.2 | Rule 1 (X heterozygosity) matches all 2141 vendor GTCs; rule 2 (X/Y intensity) differs in 12. | resolved |
| K-015 | 2026-09-28 | Legacy GTC v3 statistics | AutoCall 1.6.2.2 writes GC10 = GC50 = 0 and #calls = #no-calls = 0 in GTC v3 (it does fill LogR dev and #intensity-only). gtc2vcf's AutoConvert 1.6.3.1 preset fills them, so this is specific to 1.6.2.x. Emulated by `--preset autocall-1.6.2`; the sample summary still reports the real statistics. | resolved; cloud re-run pending |
| K-014 | 2026-09-28 | NaN sign | NaNs produced by libm (e.g. log2 of a negative extrapolated R) take the platform's default sign: + on aarch64, − on x86-64. SimurgArray always writes 0xFFC00000 (the reference's `-NAN`, x86 behaviour). The aarch64-built oracle differs in 1 locus of 9 GSA samples; oracle tests compare with NaNs canonicalised. | resolved |