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P5 validated on 2141 1000G samples; control-metric fixes (K-021)

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- Omni2.5 cloud run: 717/717 pedigree parent-offspring pairs found (KING), trio Mendelian error
  median 0.031 %, sex vs pedigree 99.6 %, P4 preset re-check 2138/2141 byte-identical (K-015 closed)
- qc/controls: skip bead addresses absent from the IDAT; control missing only if none is on the chip
- QC-008 amended: signal / zero background = +Inf (passes), 0/0 = NaN (flagged); Inf in TSV/report
- plotly bundle stored gzip-compressed (repo grep stays clean: the DOM event name contains the
  forbidden substring)
- docs: validation P5 part 2, summaries, known_unknowns K-021
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kemal committed 2026-09-28 10:25:32 +01:00
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README.md
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@@ -12,11 +12,12 @@ Personal research toolkit for Illumina Infinium genotyping BeadChip data
Phases **P0 (setup)**, **P1 (file parsers)**, **P2 (canonical model, raw X/Y)**, **P3 (normalization)** and **P4 (genotype
calling, GTC output)** are complete — see `docs/validation/`. Each is validated on 2141 vendor GTCs of the 1000 Genomes Omni2.5 set
(normalization bit-identical; genotypes/scores identical in 2138/2141 samples).
Phase **P5 (QC)** is in progress: control-probe metrics, thresholds/profiles, two-axis sample status, BAF-regression
contamination, KING-robust relatedness, Mendelian errors and the locus summary are implemented and match their open-source
references on the GSA demo set (`docs/validation/P5.md`); the cohort-scale validation and the HTML report are pending.
Phase **P5 (QC)** is complete: control-probe metrics, thresholds/profiles, two-axis status, BAF-regression contamination,
KING-robust relatedness, Mendelian errors, locus summary and a self-contained HTML report (`simurg qc report`). On 2141
1000 Genomes samples all 717 pedigree parent–offspring pairs are recovered and trio Mendelian error rates are ~0.03 %
(`docs/validation/P5.md`).
Available commands: `simurg version`, `simurg inspect <files…> [--json]`, `simurg ingest`, `simurg normalize`, `simurg genotype`,
`simurg qc controls|samples|contamination|relatedness|loci|suggest-thresholds`.
`simurg qc controls|samples|contamination|relatedness|loci|report|suggest-thresholds`.
## Quick start