sociogenomics2022

Upload the software plink on the folder Software

cd $HOME
cd Sociogenomics/Software

wget https://s3.amazonaws.com/plink1-assets/plink_linux_x86_64_20210606.zip

unzip plink_linux_x86_64_20210606.zip

Alternative command if wget is not installed in your system

curl -o plink_linux_x86_64_20210606.zip  https://s3.amazonaws.com/plink1-assets/plink_linux_x86_64_20210606.zip

Chek file permissions

chmod +rwx filename to add permissions.
chmod -rwx directoryname to remove permissions.
chmod +x filename to allow executable permissions.
chmod -wx filename to take out write and executable permissions.

chmod +x plink

./plink --help

Create symbolic links

cd $HOME/Sociogenomics
 ln -s Software/plink

./plink --help 

Clean Data and Results folder

` rm Data/. rm Results/. `

UPLOAD FILE week2.zip from Virtuale and unzip files in Data folder

cd Data/
unzip week2.zip
 mv week2/*.* ./


  rm -r __MACOSX/
  rm -r week2

cd $HOME/Sociogenomics

data type

Read Binary Plink file

head Data/hapmap-ceu.bim

head Data/hapmap-ceu.fam

.bed files are not readable!

head Data/hapmap-ceu.bed

Recode into map and ped files

./plink --bfile Data/hapmap-ceu --recode --out Results/hapmap-ceu

head Results/hapmap-ceu.map

head -1 Results/hapmap-ceu.ped

Import VCF into plink

./plink --vcf  Data/ALL.chr21.vcf.gz --make-bed --out Results/test_vcf

Select individuals

./plink --bfile Data/hapmap-ceu \
        --keep Data/list.txt \
            --make-bed --out  Results/selectedIndividuals

Select individuals with genotype at least 95% complete


./plink --bfile Data/hapmap-ceu --make-bed --mind 0.05 --out Results/highgeno

Select specific markers

./plink     --bfile Data/hapmap-ceu \
            --snps  rs9930506 \
        --make-bed \
            --out  Results/rs9930506sample

Merge genetic files

./plink --bfile Data/HapMap_founders \
--bmerge  HapMap_nonfounders \
--make-bed --out Results/merged_file

Attach a phenotype



head Data/1kg_EU_qc.fam


head Data/1kg_EU_qc.bim


head Data/BMI_pheno.txt

./plink      --bfile Data/1kg_EU_qc\
             --pheno Data/BMI_pheno.txt \
         --make-bed --out Results/1kg_EU_BMI

 head Data/1kg_EU_BMI.fam

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_hm3 --mind 0.05 --make-bed --out Results/1kg_hm3_mind005

Calculate heterozygocity


./plink --bfile Data/1kg_hm3 --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_hm3 --geno 0.05 --make-bed --out Results/1kg_hm3_geno

Allele frequency


./plink --bfile Data/1kg_hm3 --maf 0.01 --make-bed  --out Results/1kg_hm3_maf

deviation from HWE

./plink --bfile Data/1kg_hm3 --hwe 0.00001 --make-bed  --out Results/1kg_hm3_hwe

Plink QC

./plink     --bfile Data/1kg_hm3 \
        --mind 0.03 \
        --geno 0.05 \
        --maf 0.01 \
    --hwe 0.00001 \
    --exclude Data/individuals_failQC.txt \
        --make-bed  --out Results/1kg_hm3_QC      