This is a collection of useful BASH scripts and aliases to automatize the workflow in bioinformatics related research.
The scripts wrap the following software packages.
# Genotype Harmonizer
# PLINK
# SHAPEIT
# IMPUTE2
cd your_path
git clone https://github.com/qpding/wyy_dot_n_bin.git
command_or_script_name -h
Refer to the following command to make the scripts executable. In normal cases this has to be done only once after the repository is cloned.
cd path_to_the_scripts
chmod +x ./script_name.sh
Refer to this blog for a general workflow of GWAS prephasing and imputation.