1. Environment Setup

1.1. Install conda

Conda will be used to install the software needed to run this tutorial. Here are the steps used to install conda on a 64-bit computer with a Linux system using Mambaforge. For other operating systems, detailed instructions can be found here.

wget https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-Linux-x86_64.sh
bash Mambaforge-Linux-x86_64.sh -b -p "${HOME}/conda"
~/conda/bin/mamba init
source ~/.bashrc  # if zsh is being used then do `source ~/.zshrc`

1.2. Create a new environment and install software packages

mamba create -n grGWAS
mamba activate grGWAS
mamba install -c bioconda plink plink2 bcftools gcta
mamba install -c conda-forge r-base=4.3.1 r-ggplot2=3.4.2 r-gridextra=2.3 r-qqman=0.1.8