kemalandClaude Opus 5.5
874aeaef61
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. Co-Authored-By: Claude Opus 5.5 <[email protected]> Claude-Session: https://claude.ai/code/session_01814GKVzZVL3FuF3DeiZXhv
Examples
| File | What it shows |
|---|---|
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. |
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. |
The QC threshold profiles shipped with SimurgArray (src/simurg/qc/profiles/*.yaml) are the starting point for a
--qc-config file; simurg qc suggest-thresholds derives cohort-specific values. See docs/user_guide.md.