kemal
80b93e9f45
- 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
36 lines
2.3 KiB
Markdown
36 lines
2.3 KiB
Markdown
# SimurgArray
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Personal research toolkit for Illumina Infinium genotyping BeadChip data
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(IDAT → normalization → genotype calling → BAF/LRR → QC → VCF/PLINK; later CN/LOH, PGx, cluster training).
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- **SIMURGARRAY_MASTER_PLAN.md** — architecture, algorithms, roadmap
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- **SIMURGARRAY_FUNCTIONAL_SPEC.md** — 416 itemised requirements (CLI, inputs, outputs, QC, CN, PGx, methylation, edge cases)
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- `docs/validation/` — per-phase validation reports · `docs/known_unknowns.md` — findings log · `docs/research/` — background
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## Status
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Phases **P0 (setup)**, **P1 (file parsers)**, **P2 (canonical model, raw X/Y)**, **P3 (normalization)** and **P4 (genotype
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calling, GTC output)** are complete — see `docs/validation/`. Each is validated on 2141 vendor GTCs of the 1000 Genomes Omni2.5 set
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(normalization bit-identical; genotypes/scores identical in 2138/2141 samples).
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Phase **P5 (QC)** is complete: control-probe metrics, thresholds/profiles, two-axis status, BAF-regression contamination,
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KING-robust relatedness, Mendelian errors, locus summary and a self-contained HTML report (`simurg qc report`). On 2141
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1000 Genomes samples all 717 pedigree parent–offspring pairs are recovered and trio Mendelian error rates are ~0.03 %
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(`docs/validation/P5.md`).
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Available commands: `simurg version`, `simurg inspect <files…> [--json]`, `simurg ingest`, `simurg normalize`, `simurg genotype`,
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`simurg qc controls|samples|contamination|relatedness|loci|report|suggest-thresholds`.
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## Quick start
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```bash
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uv venv && uv pip install -e ".[dev]"
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uv run pytest tests/unit # no downloads needed
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bash scripts/bootstrap_refs.sh # reference open-source repos → refs/ (oracles)
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bash scripts/fetch_data.sh p0 # ~1.4 GB of public test data → data/
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bash scripts/make_oracle_gtcs.sh # builds gtc2vcf, writes oracle GTCs
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bash scripts/make_oracle_qc.sh # locus-summary oracle (BeadArrayFiles, separate venv)
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uv run pytest tests/oracle # real-data acceptance tests (add -m "not slow" to skip the long ones)
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uv run simurg inspect data/p0/gsa_v4_pgx/idats_Demo_36/idats_Demo_36/207895980019/207895980019_R03C01_Grn.idat
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```
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Vendor data files are downloaded for personal research use only and are never committed. See `THIRD_PARTY_NOTICES.md`.
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