Djinho/African_Genomics_Webtool

An python/Flask web app for exploring genetic diversity in African populations using VCF data from the 1000 Genomes Project. Features include allele frequency analysis, FST calculation, PCA visualization, and variant annotation. # African Genomics Explorer Interactive web application for exploring genetic diversity across five African populations from the 1000 Genomes Project. ## Overview This project analyzes chromosome 22 variant data from five African populations: | Population | Code | Location | Samples | |------------|------|----------|---------| | Yoruba | YRI | Ibadan, Nigeria | 108 | | Luhya | LWK | Webuye, Kenya | 99 | | Gambian | GWD | Western Division, The Gambia | 113 | | Mende | MSL | Sierra Leone | 85 | | Esan | ESN | Nigeria | 99 | **Total: 504 individuals, 134,065 variants** ## Features - **PCA Analysis**: Interactive scatter plots showing population structure (PC1 vs PC2, PC1 vs PC3) - **FST Heatmap**: Pairwise genetic differentiation between populations - **Allele Frequency Comparison**: Compare variant frequencies across any two populations ## Screenshots The webapp features a modern dark theme with interactive Plotly visualizations. ## Installation ```bash # Clone the repository git clone github.com cd African_Genomics_Webtool # Install dependencies pip install -r webapp/requirements.txt ``` ## Usage ### Running the Web Application ```bash cd webapp python app.py ``` Then open localhost in your browser. ### Reproducing the Analysis The analysis pipeline scripts are provided in numbered order: 1. `01_download_data.sh` - Download chr22 VCF from 1000 Genomes 2. `02_subset_african.sh` - Subset to African samples only 3. `03_filter_maf.sh` - Filter variants by MAF > 5% 4. `04_calculate_af.sh` - Calculate allele frequencies per population 5. `05_calculate_fst.sh` - Calculate pairwise FST values 6. `06_run_admixture.sh` - Run PCA/ADMIXTURE analysis **Requirements for pipeline:** - bcftools - vcftools - PLINK 1.9 ## Project Structure ``` African_Genomics_Webtool/ ├── webapp/ │ ├── app.py # Flask application │ ├── requirements.txt # Python dependencies │ ├── templates/ │ …