Tutorial to run GWAS including the X chromosome

Genotype data to use with the tutorial to run GWAS including the X chromosome The aim of this tutorial is to provide step-by-step instructions and scripts for performing a genome-wide association study (GWAS), starting from genotype data through to identifying the number of independent genome-wide significant SNPs. This tutorial covers the following steps, applied to both the autosomes and the X chromosome: Quality control of genotype data Imputation of genotype data Genome-wide association study (GWAS) Clumping to identify independent genome-wide significant SNPs Example genotype data is provided to use with this tutorial, or you can follow the workflow using your own genotype data This Zenodo archive provides the genotype data to use with this tutorial: Option 1: Start from raw genotype data (full workflow) Use this if you want to run the tutorial from the beginning Download the file 'Tutorial_GWAS_including_X_chromosome_raw_genotype_data.tar.gz' which contains the raw genotype data Option 2: Conduct a GWAS only Use this if you want to skip genotype QC, imputation, and ancestry checks Download the file 'Tutorial_GWAS_including_X_chromosome_start_at_GWAS.tar.gz' which contains all data needed to run the GWAS without carrying out the previous QC, imputation, and ancestry checks