bio-workflows-gwas-pipeline
End-to-end GWAS workflow from VCF to association results. Covers PLINK QC, population structure correction, and association testing for case-control or quantitative traits. Use when running genome-wide association studies.
npx skills add BioTender-max/awesome-bio-agent-skills --skill gwas-pipeline --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
## Version Compatibility Reference examples tested with: ggplot2 3.5+ Before using code patterns, verify installed versions match. If versions differ: - R: `packageVersion('<pkg>')` then `?function_name` to verify parameters - CLI: `<tool> --version` then `<tool> --help` to confirm flags If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying. # GWAS Pipeline **"Run a GWAS from my genotype data"** → Orchestrate sample/variant QC (PLINK2), population stratification (PCA), association testing (linear/logistic regression), multiple testing correction, and Manhattan/QQ plot visualization. Complete workflow for genome-wide association studies from genotype data to significant associations. ## Workflow Overview ``` VCF/PLINK files | v [1. QC Filtering] ------> Sample and variant QC | v [2. LD Pruning] --------> Independent variants for PCA | v [3. Population Structure] --> PCA for covariates | v [4. Association Testing] --> Logistic/linear regression | v [5. Results] -----------> Manhattan plot, QQ plot | v Significant associations ``` ## Step 1: Data Import and QC ### Convert VCF to PLI
- Version Compatibility
- Workflow Overview
- Step 1: Data Import and QC
- Convert VCF to PLINK
- Sample QC
- Variant QC
- Step 2: LD Pruning for PCA
- Step 3: Population Structure (PCA)
- Visualize PCA
- Step 4: Association Testing
- Case-Control (Binary Trait)
- Quantitative Trait
- With Additional Covariates
- Step 5: Results Visualization
VCF to PLINK binary format plink2 --vcf input.vcf.gz \ Or with phenotype/covariate files Calculate sample statistics plink2 --bfile study \ Remove samples with high missing rate (>5%) Check for sex discrepancies (if sex chromosome data available) plink2 --bfile study_sample_qc \ Remove related individuals (optional, requires IBD) Apply standard variant filters
What does the bio-workflows-gwas-pipeline skill do?
End-to-end GWAS workflow from VCF to association results. Covers PLINK QC, population structure correction, and association testing for case-control or quantitative traits. Use when running genome-wide association studies.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill gwas-pipeline --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From BioTender-max/awesome-bio-agent-skills, a repository with 135 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.