sociogenomics2023

Lab Week 5. Sociogenomics

Description

In this lab we will learn:

• Calculate IBS and relatedness
• Association analys

Part I . Managing files and directories. (no need after week 4, just repeating the command)

Let’s have a look a the file.

cd $HOME/Sociogenomics
rm Data/*.*

wget -O Data/lab_week4.zip https://www.dropbox.com/s/wum0okiq4dbn9p0/week4.zip?dl=0 
unzip -o -d Data/ Data/lab_week4.zip 
mv Data/week4/*.*  Data/ 
rm -r Data/week4/

Calculate IBS and relatedness

Calculate Identity By State matrix

./plink --bfile  Results/1kg_hm3_pruned \
		--keep Data/1kg_samples_EUR.txt \
		--distance --out Results/ibs_matrix

Calculate relatedness matrix

./plink --bfile Results/1kg_hm3_pruned /
		--keep Data/1kg_samples_EUR.txt /
		--make-rel --out Results/rel_matrix

Association analys

Linear additive model

./plink    	--bfile Data/1kg_EU_BMI \
        	--snps rs9674439 \
       	 	--assoc \
      	 	--linear \
      		--out Results/BMIrs9674439

Logistic additive model

./plink    	--bfile Data/1kg_EU_Overweight \
        	--snps rs9674439 \
       	 	--assoc \
      	 	--logistic \
      	 	--out Results/Overweight_rs9674439

Linear dominant analysis

./plink    	 --bfile Data/1kg_EU_BMI \
        	 --snps rs9674439 \
       	 	--assoc \
      	 	--linear dominant \
      	 	--out Results/BMIrs9674439

Genome-Wide Analysis

./plink    	--bfile Data/1kg_EU_BMI \
       	 	--assoc \
      	 	--linear \
      	 	--out Results/BMIgwas