Lab_2_Plink_and_QC

Margaret Perry

2022-04-13

Categories: Lab

Learning Objectives

  • run example GWAS using plink
  • recognize plink data formats
  • perform QC with plink
  • interpret output of plink

This Lab will cover the quality batch portion of the QC and will be using the 1_Main_scripts_QC_GWAS.txt from Marees et al A tutorial on conducting genome‐wide association studies: Quality control and statistical analysis.

Material

We will follow the tutorial published here by Marees et al A tutorial on conducting genome‐wide association studies: Quality control and statistical analysis

See the README file of the tutorial here

The majority of the code in the lab is written in Plink. Plink is a command line software that is used for quality control, population stratification, and GWAS. Below is the general syntax used for all of plink’s commands. If you get lost use the –help to get a list of available commands. For the purposes of this lab we are going to use Plink 1.9. All of plink’s commands for this lab will be run in the terminal.

Lab

Tutorial files

For this lab we will be conducting the quality control on a subset of the hapmap3 data. It will cover how to adjust for missingness, relatedness, MAF, and HWE. Feel free to check back with the tutorial paper as a reference for definitions and additional command explanations. We will only be doing the first part of the tutorial, 1_QC_GWAS. The 1_QC_GWAS folder will be our working directory for the lab so be sure to navigate there before you begin.

For convenience, I’ve copied the tutorial’s scripts below

1. GWAS QC

References

Marees, AT, de Kluiver, H, Stringer, S, et al. A tutorial on conducting genome‐wide association studies: Quality control and statistical analysis. Int J Methods Psychiatr Res. 2018; 27:e1608. https://doi.org/10.1002/mpr.1608

Reuse

Text and figures are licensed under Creative Commons Attribution CC BY 4.0. The source code is licensed under MIT.

Suggest changes

If you find any mistakes (including typos) or want to suggest changes, please feel free to edit the source file of this page on Github and create a pull request.

Citation

For attribution, please cite this work as

Margaret Perry (2022). Lab_2_Plink_and_QC. BIOS 25328 Cancer Genomics Class Notes. /post/2022/04/13/lab-2-plink-and-qc/

BibTeX citation

@misc{
  title = "Lab_2_Plink_and_QC",
  author = "Margaret Perry",
  year = "2022",
  journal = "BIOS 25328 Cancer Genomics Class Notes",
  note = "/post/2022/04/13/lab-2-plink-and-qc/"
}