lab 3

bios25328

lab

In this lab, you will run all the steps of a GWAS analysis using the Marees et al tutorial.

Published

April 5, 2024

Modified

April 2, 2024

Instructions

Read and summarize in a few sentences this GWAS tutorial paper https://onlinelibrary.wiley.com/doi/10.1002/mpr.1608
Download plink from LINK (choose the one corresponding to your operating system. If running on posit.cloud, you should choose the linux version even if you are accessing posit from a different operating system)
Create a github user if you don’t already have one
Git clone the tutorial from the command line (run git clone <https://github.com/MareesAT/GWA_tutorial.git> on the terminal). You will need to unzip files that look like *.zip
run the QC and Association components of the tutorial
- 1_Main_script_QC_GWAS.txt and 3_Main_script_association_GWAS.txt
  - you may want to download the hapmap data from here https://uchicago.box.com/s/hawatrohw6fthytguaww83njrf5i6ace
- you may need to download plink (https://www.cog-genomics.org/plink/1.9/)
- The tutorial is designed so that you need to run all the steps but since 2_Population_stratification.txt is quite computationally time consuming, you can skip it and just download the files you need to run associations here https://uchicago.box.com/s/ux2xkab6zhth0csazixqoj98xtjh7h0x

Notes

Some modifications to the code may be needed. Use them if you encounter errors.

Relatedness.R needs to change lines 7 and 15 to

legend(1,1, xjust=1, yjust=1, legend=levels(factor(relatedness$RT)), pch=16, col=c(4,3))
legend(0.02,1, xjust=1, yjust=1, legend=levels(factor(relatedness$RT)), pch=16, col=c(4,3))

line 31 of 2_Main_script_MDS.txt replace

plink --bfile ALL.2of4intersection.20100804.genotypes --set-missing-var-ids @:#[b37]\$1,\$2 --make-bed --out ALL.2of4intersection.20100804.genotypes_no_missing_IDs

with

plink --bfile ALL.2of4intersection.20100804.genotypes --set-missing-var-ids '@:#[b37]$1,$2' --make-bed --out ALL.2of4intersection.20100804.genotypes_no_missing_IDs

line 144 in 2_Main_script_MDS.txt replace

(base) haekyungim@Im-Lab-016 1_QC_GWAS % cat race_1kG14.txt racefile_own.txt | sed -e '1i\FID IID race' > racefile.txt
sed: 1: "1i\FID IID race
": extra characters after \ at the end of i command
(base) haekyungim@Im-Lab-016 1_QC_GWAS % cat race_1kG14.txt racefile_own.txt | sed -e '1i\
FID IID race' > racefile.txt

install qqman in R and comment out first line on Manhattan_plot.R and QQ_plot.R

##install.packages("qqman",repos="http://cran.cnr.berkeley.edu/",lib="~" ) # location of installation can be changed but has to correspond with the library location 
##library("qqman",lib.loc="~")  
library("qqman")

Questions

Using the output from the tutorial or using the commands you learned from it, answer the following questions. Show the command you used to create the result.

How many individuals are in the genotype file you downloaded? (5 pts)
Explain the contents of .fam, .bim, .bed files (5 pts)
Write the captions for the figures generated by the commands in 1_Main_script_QC_GWAS.txt and 3_Main_script_association_GWAS (5 pts per figure caption)
Explain what you accomplished with the tutorial and explain the results/figures you obtained. (20 pts)

--- title: lab 3 date: 2024-04-05 categories: - bios25328 - lab date-modified: last-modified description: In this lab, you will run all the steps of a GWAS analysis using the Marees et al tutorial. --- ## Instructions - [ ] Read and summarize in a few sentences this GWAS tutorial paper [https://onlinelibrary.wiley.com/doi/10.1002/mpr.1608](https://onlinelibrary.wiley.com/doi/10.1002/mpr.1608) - [ ] Download plink from [LINK](https://www.cog-genomics.org/plink/1.9/) (choose the one corresponding to your operating system. If running on posit.cloud, you should choose the linux version even if you are accessing posit from a different operating system) - [ ] Create a github user if you don’t already have one - [ ] Git clone the tutorial from the command line (run `git clone <https://github.com/MareesAT/GWA_tutorial.git`> on the terminal). You will need to unzip files that look like *.zip - [ ] run the QC and Association components of the tutorial - 1_Main_script_QC_GWAS.txt and 3_Main_script_association_GWAS.txt - you may want to download the hapmap data from here [https://uchicago.box.com/s/hawatrohw6fthytguaww83njrf5i6ace](https://uchicago.box.com/s/hawatrohw6fthytguaww83njrf5i6ace) - you may need to download plink ([https://www.cog-genomics.org/plink/1.9/](https://www.cog-genomics.org/plink/1.9/)) - The tutorial is designed so that you need to run all the steps but since 2_Population_stratification.txt is quite computationally time consuming, you can skip it and just download the files you need to run associations here [https://uchicago.box.com/s/ux2xkab6zhth0csazixqoj98xtjh7h0x](https://uchicago.box.com/s/ux2xkab6zhth0csazixqoj98xtjh7h0x) ## Notes > Some modifications to the code may be needed. Use them if you encounter errors. Relatedness.R needs to change lines 7 and 15 to ```r legend(1,1, xjust=1, yjust=1, legend=levels(factor(relatedness$RT)), pch=16, col=c(4,3)) legend(0.02,1, xjust=1, yjust=1, legend=levels(factor(relatedness$RT)), pch=16, col=c(4,3)) ``` line 31 of 2_Main_script_MDS.txt replace ```bash plink --bfile ALL.2of4intersection.20100804.genotypes --set-missing-var-ids @:#[b37]\$1,\$2 --make-bed --out ALL.2of4intersection.20100804.genotypes_no_missing_IDs ``` with ```bash plink --bfile ALL.2of4intersection.20100804.genotypes --set-missing-var-ids '@:#[b37]$1,$2' --make-bed --out ALL.2of4intersection.20100804.genotypes_no_missing_IDs ``` line 144 in 2_Main_script_MDS.txt replace ```bash (base) haekyungim@Im-Lab-016 1_QC_GWAS % cat race_1kG14.txt racefile_own.txt | sed -e '1i\FID IID race' > racefile.txt sed: 1: "1i\FID IID race ": extra characters after \ at the end of i command (base) haekyungim@Im-Lab-016 1_QC_GWAS % cat race_1kG14.txt racefile_own.txt | sed -e '1i\ FID IID race' > racefile.txt ``` install qqman in R and comment out first line on Manhattan_plot.R and QQ_plot.R ```bash ##install.packages("qqman",repos="http://cran.cnr.berkeley.edu/",lib="~" ) # location of installation can be changed but has to correspond with the library location ##library("qqman",lib.loc="~") library("qqman") ``` ## Questions Using the output from the tutorial or using the commands you learned from it, answer the following questions. Show the command you used to create the result. 1. How many individuals are in the genotype file you downloaded? (5 pts) 2. Explain the contents of `.fam`, `.bim`, `.bed` files (5 pts) 3. Write the captions for the figures generated by the commands in 1_Main_script_QC_GWAS.txt and 3_Main_script_association_GWAS (5 pts per figure caption) 4. Explain what you accomplished with the tutorial and explain the results/figures you obtained. (20 pts)