sociogenomics2023

Lab Week 4. Sociogenomics

Description

In this lab we will learn:

• Compute descripitve statistics with PLINK on genetic files
• Quality control procedure with plink
• Run association analysis with PLINK
• Select independent SNPS
• compute Principal Components Analysis in PLINK

Part I . Managing files and directories.

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/

 head Data/1kg_EU_BMI.fam

how many observations?

 wc -l Data/1kg_EU_BMI.fam

how many variants?

 wc -l Data/1kg_EU_BMI.bim

Descriptive Statistics

Allele frequency

 ./plink --bfile Data/hapmap-ceu  --freq --out Results/Allele_Frequency

head Results/Allele_Frequency.frq 

Missing values

individuals

./plink --bfile Data/hapmap-ceu --missing --out Results/missing_data

variants

head Data/missing_data.imiss

Filter females

./plink     --bfile Data/hapmap-ceu \
            --filter-females \
            --make-bed \
       	 	--out Results/hapmap_filter_females

Quality control

./plink --bfile Data/1kg_EU_BMI \
		--mind 0.05 \
		--make-bed \
		--out Results/1kg_hm3_mind005

Calculate heterozygocity

./plink --bfile Data/1kg_EU_BMI \
		--het --out Results/1kg_hm3_het

Check discordant sex

./plink --bfile Data/hapmap-ceu \
		--check-sex \
		--out Results/hapmap_sexcheck 

Low call-rate SNPS

./plink --bfile Data/1kg_EU_BMI \
		--geno 0.05 \
		--make-bed \
		--out Results/1kg_hm3_geno

Allele frequency

./plink --bfile Data/1kg_EU_BMI \
	 	--maf 0.01 \
		--make-bed  --out Results/1kg_hm3_maf

deviation from HWE

./plink --bfile Data/1kg_EU_BMI \
	 	--hwe 0.00001 \
		--make-bed  --out Results/1kg_hm3_hwe

PLINK QC. combine different commands in one go

./plink     --bfile Data/1kg_EU_BMI \
       	--mind 0.03 \
       	--geno 0.05 \
       	--maf 0.01 \
    	--hwe 0.00001 \
        --make-bed  --out Results/1kg_hm3_QC      
			

Select independent SNPS

Calculate linkage disequilibrium

./plink --bfile Data/hapmap-ceu \
	 	--ld rs2883059 rs2777888 \
		--out Results/ld_example

Calculate independent SNPs (Pruning)

./plink 	 --bfile Results/1kg_EU_BMI --maf 0.01 \
        	--indep-pairwise 50 5 0.2 \
        	--out  Results/1kg_hm3_qc_pruned

Select from original sample independent SNPs

./plink		--bfile  Results/1kg_EU_BMI \
			--extract Results/1kg_hm3_qc_pruned.prune.in \
			--make-bed \
 			--out  Results/1kg_hm3_pruned
		
		

Calculate PCA

./plink --bfile  Results/1kg_hm3_pruned \
		--pca 10 \
		--out  Results/1kg_pca