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SimurgArray: master plan, repo scaffolding and data/ref fetch scripts

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Phase 0 deliverables: full technical specification and roadmap
(SIMURGARRAY_MASTER_PLAN.md), CLAUDE.md, bootstrap script for reference
open-source repos and tiered dataset fetch script with checksums.

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 2026-09-27 15:20:06 +01:00
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README.md
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# 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).
Start with **SIMURGARRAY_MASTER_PLAN.md** (full specification and roadmap).
```bash
bash scripts/bootstrap_refs.sh # clone reference open-source repos into refs/
bash scripts/fetch_data.sh p0 # download small test datasets into data/
```