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P8 complete: scientific validation on GSE165845 vs NYGC 30x and GIAB HG001
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360 GSA arrays (120 1000 Genomes individuals x 3 replicates): concordance 0.9934 vs
NYGC 30x (0.9958 on sites in both sets), 0.9985 vs GIAB HG001 v4.2.1 (non-ref F1
0.997), replicate concordance 0.9966; allele-swap sites 0.016 %; 358/360 replicate
pairs detected as duplicates. Plan §16.5 metrics in docs/validation/P8.md (K-024).

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 19:47:34 +01:00
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README.md
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@@ -24,6 +24,9 @@ On the GSA demo, genotypes match gtc2vcf and GTCtoVCF with zero unexplained diff
Phase **P7 (differential testing)** is complete: `simurg compare` (EXACT/NEAR/DISCREPANCY/UNKNOWN per field and
locus class, every discrepancy listed, HTML dashboard) and a nightly run on the Pi (GSA vs gtc2vcf, Omni2.5 subset vs
vendor GTCs, VCF regression) — `docs/validation/P7.md`.
Phase **P8 (scientific validation)** is complete: on GEO GSE165845 (360 GSA arrays, 120 1000 Genomes individuals ×
3 replicates) genotype concordance is 0.9934 vs NYGC 30x WGS, 0.9985 vs GIAB HG001 v4.2.1 (non-ref F1 0.997), and
0.9966 between replicates — `docs/validation/P8.md`.
Available commands: `simurg version`, `simurg inspect <files…> [--json]`, `simurg ingest`, `simurg normalize`, `simurg genotype`,
`simurg qc controls|samples|contamination|relatedness|loci|report|suggest-thresholds`, `simurg gtc-to-vcf`,
`simurg export plink|bedgraph|finalreport|locus-summary`, `simurg compare`.