kemalandClaude Opus 5.5
2e8478cc6a
- gtc-to-vcf --info-fields ASSAY_TYPE,NORM_BIN,GENTRAIN,CLUSTER_SEP,ILMN_STRAND,PROBE_IDS (--egt) and --extra-format X,Y,NORMX,NORMY,THETA,R, in per-sample VCFs and the --merge BCF (OUT-012, plan §8.3); equal to gtc2vcf's values (THETA/R missing where both normalized intensities are 0, K-023) - --merge-snv-indel (OUT-021, EDGE-013): alleles extended to the longest REF; SNV probes read the base at POS - --auxiliary-loci (OUT-035, EDGE-015): rules (a)-(e), E_AUX_INVALID; rule (d) uses the last plus-strand base for minus-strand designs (spec amended, as GTCtoVCF) - export plink --format bed|pgen|both: PLINK 2 fixed-width .pgen/.pvar/.psam; plink2 reads it back to a .bed byte-identical to ours - cohort store keeps raw/normalized intensities for the BCF path; tests (unit + gtc2vcf oracle); docs Co-Authored-By: Claude Opus 5.5 <[email protected]> Claude-Session: https://claude.ai/code/session_01814GKVzZVL3FuF3DeiZXhv
44 lines
3.0 KiB
Markdown
44 lines
3.0 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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Phase **P6 (outputs)** is complete: `simurg gtc-to-vcf` (plus-strand harmonisation with audit, merged multi-probe
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sites, per-sample VCF.gz + tabix or a cohort BCF + CSI, optional INFO/intensity fields, SNV+indel merging, MNV
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auxiliary loci) and `simurg export plink|bedgraph|finalreport|locus-summary` (PLINK 1 `.bed` and PLINK 2 `.pgen`).
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On the GSA demo, genotypes match gtc2vcf and GTCtoVCF with zero unexplained differences and PLINK files match plink2
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(`docs/validation/P6.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`, `simurg gtc-to-vcf`,
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`simurg export plink|bedgraph|finalreport|locus-summary`.
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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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bash scripts/fetch_data.sh p6 # GRCh38 FASTA (~0.9 GB download, 3.1 GB unpacked)
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bash scripts/make_oracle_vcf.sh # gtc2vcf oracle VCF for the P6 tests
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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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