AfriGen-D/african-genomics-short-course-2025

# AfriGen-D Imputation Service Tutorial Tutorial materials for the **1st African Genomics Short Course - Cape Town 2025**. **View Tutorial Online:** ## Overview This repository contains a hands-on tutorial for using the AfriGen-D Imputation Service, a free web-based platform for African genotype imputation. ## Contents - `Tutorial-AfriGenD-Imputation-Service.md` - Complete tutorial guide - `data/sparse_peaks_dense.vcf.gz` - Sample genotype data (VCF format, chromosome 22) - `data/1k_afr_661_samples_phenotype.txt` - Sample phenotype file for GWAS ## What You'll Learn 1. Creating an account and navigating the platform 2. Running genotype imputation with the H3Africa V6HC-S reference panel 3. Using the Allele Switch Checker for quality control 4. Performing VCF Liftover between genome builds 5. Running GWAS analysis on sparse vs imputed data 6. Interpreting imputation quality metrics and GWAS results ## Requirements - Web browser (Chrome, Firefox, Safari, or Edge) - Free account at impute.afrigen-d.org ## Support - Documentation: afrigen-d.org - Help Desk: helpdesk.afrigen-d.org - Email: support@bioinformaticsinstitute.africa ## License This tutorial is provided for educational purposes as part of the African Genomics Short Course.