Genetic association studies: Pipelines and useful functions

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.

1. Genotyping quality control

Genotype quality control for genotyping arrays with plinkQC

2. Imputation and phasing

Phasing and imputation of plink formated genotype calls using phaseit and impute2: here.

3. reference

Shell scripts for downloading and processing of reference data sets used in human genetic association studies.

  1. 1000Genomes

4. GWAS

Functions for processing and depicting of genome-wide association analysis results, find them here

5. utils

Generally useful functions for plotting and data processing, find them here.