Skip to content

FILE_STRUCTURE.md

Latest commit

 

History

History
137 lines (112 loc) · 4.72 KB

FILE_STRUCTURE.md

File metadata and controls

137 lines (112 loc) · 4.72 KB

AA-GWAS Analysis Pipeline - File Structure

Repository Organization

AA-GWAS/
├── .github/
│   ├── ISSUE_TEMPLATE/
│   │   ├── bug_report.yml           # Bug report template
│   │   └── feature_request.yml      # Feature request template
│   └── workflows/
│       └── ci.yml                    # GitHub Actions CI/CD
│
├── .gitignore                        # Git ignore patterns
├── CHANGELOG.md                      # Version history and changes
├── CITATION.md                       # Citation information
├── CONTRIBUTING.md                   # Contribution guidelines
├── FAQ.md                            # Frequently asked questions
├── LICENSE                           # MIT License
├── README.md                         # Main documentation
├── QUICKSTART.md                     # Quick start guide
│
├── config.example                    # Example configuration file
├── init_repo.sh                      # Repository initialization script
├── install.sh                        # Installation script
│
├── gwas_analysis_pipeline.sh         # Main pipeline (18 steps)
├── extract_individuals.sh            # Individual list extraction
├── extract_top_snps.py              # Python SNP extraction utility
└── generate_plots.py                # Visualization generation utility

File Descriptions

Documentation Files

  • README.md: Comprehensive project documentation with features, usage, and examples
  • QUICKSTART.md: Step-by-step guide to get started in minutes
  • FAQ.md: Common questions and troubleshooting
  • CHANGELOG.md: Detailed version history and release notes
  • CITATION.md: How to cite this work and dependencies
  • CONTRIBUTING.md: Guidelines for contributors
  • LICENSE: MIT License terms

Core Scripts

  • gwas_analysis_pipeline.sh: Main 18-step GWAS analysis pipeline

    • Quality control (steps 1-9)
    • Population structure (steps 10-12)
    • Association analysis (steps 13-15)
    • Export and visualization (steps 16-18)

  • extract_individuals.sh: Standalone script to quickly extract individual lists

    • Detailed list with headers
    • ID-only list
    • Cases, controls, males, females

  • extract_top_snps.py: Python utility for efficient SNP extraction

    • Handles large files (>800K SNPs)
    • Top 100, top 1000 SNPs
    • Genome-wide significant (p<5e-8)
    • Suggestive (p<1e-5)

  • generate_plots.py: Visualization generation

    • Manhattan plots
    • Q-Q plots with genomic inflation
    • PCA plots
    • Missingness distribution plots

Configuration & Setup

  • config.example: Template configuration file with all parameters
  • install.sh: Automated installation and dependency checking
  • init_repo.sh: Git repository initialization helper

GitHub Integration

  • .github/workflows/ci.yml: Continuous integration

    • ShellCheck for bash scripts
    • Python linting
    • Compatibility testing (Python 3.6-3.11)

  • .github/ISSUE_TEMPLATE/: Issue templates

    • Bug reports
    • Feature requests

  • .gitignore: Excludes large data files and intermediate results

Output Structure (Created by Pipeline)

When you run the pipeline, it creates:

analysis_results/
├── individuals_*.txt              # Individual lists
├── qc/                           # Quality control results
│   ├── qc_summary.txt
│   ├── *_pca.eigenvec
│   ├── *_ibd.genome
│   └── *_qc3_hwe.{bed,bim,fam}
├── association/                  # Association results
│   ├── *_assoc_noQC.*
│   ├── *_assoc_withQC.*
│   ├── *_logistic_3PCs.*
│   ├── *_logistic_10PCs.*
│   ├── top_100_snps.txt
│   ├── top_1000_snps.txt
│   ├── genome_wide_significant_snps_5e-8.txt
│   └── suggestive_snps_1e-5.txt
├── plots/                        # Visualization
│   ├── manhattan_plot_*.png
│   ├── qq_plot_*.png
│   ├── pca_plot.png
│   └── missingness_plots.png
├── reports/                      # Summary reports
│   └── GWAS_Analysis_Final_Report.txt
└── logs/                         # SLURM/execution logs

File Sizes

Approximate sizes:

  • Documentation: ~40 KB total
  • Scripts: ~55 KB total
  • Repository (no data): <100 KB
  • With results (depends on dataset): 100 MB - 10 GB

Maintenance

  • Update CHANGELOG.md for each release
  • Keep README.md in sync with code changes
  • Update FAQ.md as questions arise
  • Review and merge ISSUE_TEMPLATE suggestions

Last Updated: December 11, 2025