Welcome to the homepage for all content related to Quality-Control for GWAS: Part 1 for the GINGER Program! You may navigate to the individual parts within Quality-Control for GWAS: Part 1 by clicking on the tabs below. There are four parts to this module with corresponding videos and learning checks available as you click each link.
Learning Objectives
- How do genotyping arrays work?
- Show the use of genotyping array in GWAS
- Identify potential source of bias that come from genotyping arrays (missingness, batch effects)
- Define batch effects and explain why we conduct QC
- List and define different types of sample quality control (Missingness, sex check, identifying related samples, inbreeding coefficient)
- Infer potential errors that would arise from poor sample quality control
- List and define different types of variant quality control (Missingness, HWE, MAF)
- Infer potential errors that would arise from poor quality variant control
- Overview of parameters threshold for rare variant QC
Lecture Videos and Learn Checks
Below is an overview of this module. Please watch the required videos and complete the corresponding learning checks to self-assess your comprehension of the key concepts covered. After you have completed the videos and learning checks, please complete the corresponding assignment.