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)

src/simurg/qc/profiles/genotyping.yaml

@@ -0,0 +1,21 @@
+# Starting point for review, not a truth (spec QC-024): recalibrate on your own data with
+# `simurg qc suggest-thresholds`. For LCG/HTS genotyping chips.
+qc:
+  report:
+    callRate: 0.98
+    logRDev: 0.20
+    stainingGreen: 5
+    stainingRed: 5
+    extensionGreen: 5
+    extensionRed: 5
+    hybGreenHighMed: 1
+    hybGreenMediumLow: 1
+    targetRemovalI: 1
+    restoration: null
+    stringency: 2
+    nonSpecificBindingGreen: 1
+    nonSpecificBindingRed: 1
+    npGreen: 5
+    npRed: 5
+    assayControl: 1
+    bgOffset: 3000

src/simurg/qc/profiles/genotyping_ex.yaml

@@ -0,0 +1,21 @@
+# Starting point for review, not a truth (spec QC-024): recalibrate on your own data with
+# `simurg qc suggest-thresholds`. For EX-format genotyping chips (provisional, OQ-046).
+qc:
+  report:
+    callRate: 0.98
+    logRDev: 0.20
+    stainingGreen: 5
+    stainingRed: 5
+    extensionGreen: 5
+    extensionRed: 5
+    hybGreenHighMed: 1
+    hybGreenMediumLow: 1
+    targetRemovalI: 1
+    restoration: null
+    stringency: 2
+    nonSpecificBindingGreen: 1
+    nonSpecificBindingRed: 1
+    npGreen: 5
+    npRed: 5
+    assayControl: 1
+    bgOffset: 3000

src/simurg/qc/profiles/genotyping_example.yaml

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+# Alternative example values from the reference documentation (spec QC-024). Starting point for review only.
+qc:
+  report:
+    callRate: 0.98
+    logRDev: 0.15
+    stainingGreen: 5
+    stainingRed: 5
+    extensionGreen: 5
+    extensionRed: 5
+    hybGreenHighMed: 1.25
+    hybGreenMediumLow: 1.25
+    targetRemovalI: 5
+    restoration: null
+    stringency: 1.5
+    nonSpecificBindingGreen: 5
+    nonSpecificBindingRed: 5
+    npGreen: 5
+    npRed: 5
+    assayControl: 1
+    bgOffset: 3000

src/simurg/qc/profiles/methylation_epic.yaml

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+# Methylation EPIC profile (spec QC-024). Methylation metrics are computed from v2 on.
+qc:
+  report:
+    stainingGreen: 5
+    stainingRed: 5
+    extensionGreen: 5
+    extensionRed: 5
+    hybGreenHighMed: 1
+    hybGreenMediumLow: 1
+    targetRemovalI: 1
+    targetRemovalII: 1
+    restoration: 0
+    npGreen: 5
+    npRed: 5
+    bisulfiteConversionIGreen: 1
+    bisulfiteConversionIRed: 1
+    bisulfiteConversionIGreenBg: 1
+    bisulfiteConversionIRedBg: 1
+    bisulfiteConversionII: 1
+    bisulfiteConversionIIBg: 1
+    specificityIGreen: 1
+    specificityIRed: 1
+    specificityII: 1
+    specificityIIBg: 1
+    bgOffset: 3000

src/simurg/qc/profiles/methylation_msa.yaml

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+# Methylation MSA profile (spec QC-024). Methylation metrics are computed from v2 on.
+qc:
+  report:
+    stainingGreen: 5
+    stainingRed: 5
+    extensionGreen: 5
+    extensionRed: 5
+    hybGreenHighMed: 1
+    hybGreenMediumLow: 1
+    targetRemovalI: 1
+    targetRemovalII: 1
+    restoration: 0
+    npGreen: 2.5
+    npRed: 3
+    bisulfiteConversionIGreen: 1
+    bisulfiteConversionIRed: 1
+    bisulfiteConversionIGreenBg: 0.5
+    bisulfiteConversionIRedBg: 0.5
+    bisulfiteConversionII: 0.5
+    bisulfiteConversionIIBg: 0.5
+    specificityIGreen: 1
+    specificityIRed: 1
+    specificityII: 1
+    specificityIIBg: 1
+    bgOffset: 3000