# SimurgArray

Personal research toolkit for Illumina Infinium genotyping BeadChip data
(IDAT → normalization → genotype calling → BAF/LRR → QC → VCF/PLINK; later CN/LOH, PGx, cluster training).

- **SIMURGARRAY_MASTER_PLAN.md** — architecture, algorithms, roadmap
- **SIMURGARRAY_FUNCTIONAL_SPEC.md** — 416 itemised requirements (CLI, inputs, outputs, QC, CN, PGx, methylation, edge cases)
- `docs/validation/` — per-phase validation reports · `docs/known_unknowns.md` — findings log · `docs/research/` — background

## Status

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 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`).
Phase **P6 (outputs)** is complete: `simurg gtc-to-vcf` (plus-strand harmonisation with audit, merged multi-probe
sites, per-sample VCF.gz + tabix or a cohort BCF + CSI, optional INFO/intensity fields, SNV+indel merging, MNV
auxiliary loci) and `simurg export plink|bedgraph|finalreport|locus-summary` (PLINK 1 `.bed` and PLINK 2 `.pgen`).
On the GSA demo, genotypes match gtc2vcf and GTCtoVCF with zero unexplained differences and PLINK files match plink2
(`docs/validation/P6.md`).
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`.

## Quick start

```bash
uv venv && uv pip install -e ".[dev]"
uv run pytest tests/unit                  # no downloads needed
bash scripts/bootstrap_refs.sh            # reference open-source repos → refs/ (oracles)
bash scripts/fetch_data.sh p0             # ~1.4 GB of public test data → data/
bash scripts/make_oracle_gtcs.sh          # builds gtc2vcf, writes oracle GTCs
bash scripts/make_oracle_qc.sh            # locus-summary oracle (BeadArrayFiles, separate venv)
bash scripts/fetch_data.sh p6             # GRCh38 FASTA (~0.9 GB download, 3.1 GB unpacked)
bash scripts/make_oracle_vcf.sh           # gtc2vcf oracle VCF for the P6 tests
uv run pytest tests/oracle                # real-data acceptance tests (add -m "not slow" to skip the long ones)
uv run simurg inspect data/p0/gsa_v4_pgx/idats_Demo_36/idats_Demo_36/207895980019/207895980019_R03C01_Grn.idat
```

Vendor data files are downloaded for personal research use only and are never committed. See `THIRD_PARTY_NOTICES.md`.