kemalandClaude Opus 5.5
0fe3977187
- GTCtoVCF (Apache-2.0, 36 GSA samples, merged sites): 23.66 M identical calls; every difference named (intensity-only probes merged by the oracle, its opposite-strand indel bug EDGE-012, normalisation-based grouping, OUT-018 ploidy); indel representations identical, including 144 gtc2vcf cannot resolve - validate_p6_vcf.py: rule-based categories (--bpm for [I/D]/[D/I] detection) - docs: validation P6 complete, README status Co-Authored-By: Claude Opus 5.5 <[email protected]> Claude-Session: https://claude.ai/code/session_01814GKVzZVL3FuF3DeiZXhv
2.9 KiB
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) and simurg export plink|bedgraph|finalreport|locus-summary.
On the GSA demo, genotypes match gtc2vcf and GTCtoVCF with zero unexplained differences and PLINK files match plink2
(docs/validation/P6.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.
Quick start
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.