The following repository contains pipelines and functions I found useful while working on genome-wide association studies. This work includes links to detailed genotype quality control with plinkQC, reference panel download, phasing and imputation, genome-wide association studies and analysis thereof.
All scripts can simply be sourced to access the relevant functions. Alternatively, the modules package offers flexible and tidy integration of R source files. Application of functions in this repository via modules in e.g. ukbb-fd.
Genotype quality control for genotyping arrays with plinkQC
Phasing and imputation of plink formated genotype calls using phaseit and impute2: here.
Shell scripts for downloading and processing of reference data sets used in human genetic association studies.
Functions for processing and depicting of genome-wide association analysis results, find them here
Generally useful functions for plotting and data processing, find them here.