GWAS Workshop @ VT

This workshop is intended to give students an introduction to running GWAS in R. It covers genotyping quality control, single marker regression, whole genome regression, and advanced topics for GWAS on multidimensional datasets. Below are the course materials for the sections I taught.

Link to the course website

Schedule

• Day 1 (6/24/19): Single marker regression GWAS
  • 9:00-10:30 - Kinship & Linear mixed models
  • 10:30-12:00 - Quality control, Single marker regression GWAS, & Multiple testing (pptx)
  • 12:00-13:30 - Lunch break
  • 13:30-15:30 - Lab: Single marker regression GWAS using rrBLUP and GAPIT (Materials)
• Day 2 (6/25/19): Bayesian whole-genome regression GWAS
  • 9:00-10:30 - Bayesian statistics in a nutshell
  • 10:30-12:00 - Bayesian whole-genome regression (Bayesian alphabet) for GWAS (pdf)
  • 12:00-13:30 - Lunch break
  • 13:30-15:30 - Lab: Bayesian whole-genome regression GWAS using rrBLUP, gaston, and BGLR (Materials)
• Day 3 (6/26/19): Advanced topics: Genetic analysis of image-based high-throughput phenotyping data
  • 9:00-10:00 - Time series GWAS (pptx)
  • 10:00-11:00 - Bayesian confirmatory factor analysis and Bayesian network for high-dimensional phenotypic data
  • 11:00-12:00 - Network GWAS using structural equation model
  • 12:00-13:30 - Lunch break
  • 13:30-15:30 - Lab: Bring your own GWAS data