kemal
f11b39b5a3
docs/user_guide.md (install, inputs, complete run, commands, presets, QC, outputs, accuracy, limitations, troubleshooting), examples/gsa_demo.sh (end-to-end run on the public GSA demo, verified on the Pi), examples/sample_sheet.csv, CHANGELOG.md; version 1.0.0.
10 lines
926 B
Markdown
10 lines
926 B
Markdown
# Examples
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| File | What it shows |
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| `gsa_demo.sh` | End-to-end run on the public 36-sample GSA v4 PGx demo: `genotype` (GTC + QC) → `qc report` → `gtc-to-vcf` (per-sample VCF and cohort BCF) → `export plink/bedgraph/finalreport` → `compare`. Needs `scripts/fetch_data.sh p0` and `p6`. `bash examples/gsa_demo.sh results/gsa_demo 6` runs on the first 6 samples only. |
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| `sample_sheet.csv` | Sample-sheet layout: key columns `SentrixBarcode_A`/`SentrixPosition_A`, reported sex, trio (`Parent1`/`Parent2`, used for Mendel errors), a replicate, and a free column (`Batch`) that is carried into the QC table. The sample identities in it are illustrative, not the real demo samples. |
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The QC threshold profiles shipped with SimurgArray (`src/simurg/qc/profiles/*.yaml`) are the starting point for a
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`--qc-config` file; `simurg qc suggest-thresholds` derives cohort-specific values. See `docs/user_guide.md`.
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