Learning Objectives
- 7.1 Understand how do genotyping arrays work. Be able to show the use of genotyping array in GWAS. List differences of genotyping arrays in GWAS studies (multiple array platforms, ancestries, genomic build). Identify potential source of bias that come from genotyping arrays (missingness, batch effects)
- 7.2 List and define different types of variant quality control (Missingness, HWE, MAF, Imputations Score, batch effects) Infer potential errors that would arise from poor quality variant control. Identify functions to apply variant quality control with Plink. Diagnositc plots if applicable
- 7.3 Provide an overview of parameters threshold for rare variant QC
- 7.4 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. Identify functions to apply sample quality control with Plink
Lecture Videos and Learning Checks
Below is an overview of this module. Using the “Next” button below, please watch the required videos and complete the corresponding learning checks to self-assess your comprehension of the key concepts covered. You may also download the videos directly by clicking on the titles. After you have completed the videos and learning checks, please complete the corresponding assignment.