sociogenomics2023

Lab 2. Getting started with Plink

Installing Plink in your system

PLINK is a free, open-source software package for genomic data analysis. It was originally designed for analyzing genetic association studies, particularly for case-control studies and family-based studies. PLINK can perform various tasks related to genetic data analysis, including data management, quality control, association analysis, haplotype analysis, and population stratification correction.

PLINK is widely used in the field of human genetics and has been cited in numerous scientific publications. It is compatible with various file formats commonly used in genetics research, such as VCF, BED, and PED formats. PLINK is available for download on the project’s website and is actively maintained by a team of developers.

Let’s start from our home directory and change directory to Sociogenomics/Software

cd $HOME
cd Sociogenomics/Software

PLINK is available from here: We use (for now) PLINK 1.9. Now we can download the linux version in our system

wget https://s3.amazonaws.com/plink1-assets/plink_linux_x86_64_20230116.zip
unzip plink_linux_x86_64_20230116.zip

let’s check file permission. We need to make plink executable to use it as software

ls -l

Check 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.

This is how we make the file executable

chmod +x plink

we can now execute the software using ./ in front of the file

./plink --help

Create symbolic links

A symbolic link, also known as a symlink or a soft link, is a type of file that acts as a pointer or reference to another file or directory in a file system.

When a symbolic link is created, it contains the path to the file or directory that it points to. When a user accesses the symbolic link, the file system follows the link and accesses the file or directory that it points to, as if the user had accessed it directly.

Symbolic links are often used in Unix-based operating systems, such as Linux or macOS, to create shortcuts to frequently used files or directories, or to provide a simpler or more intuitive file structure. They can also be used to create multiple paths to the same file or directory, or to enable compatibility between different versions of software.

cd $HOME/Sociogenomics
ln -s Software/plink

Now we can access PLINK from this directory

pwd
./plink --help 

Upload the file `week2.zip` and unzip files in Data folder

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


  rm -r __MACOSX/
  rm -r week2

cd $HOME/Sociogenomics

How to read PLINK files

data type

Read Binary PLINK file

we start with PLINK binary files

.bim file contains info on the markers
```
head Data/hapmap-ceu.bim
```
.fam file contains info on the individuals
```
head Data/hapmap-ceu.fam
```
.bed files are not readable!
```
head Data/hapmap-ceu.bed
```
Recode PLINK file

Recode into map and ped files

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

.map file contains info on the markers

head Results/hapmap-ceu.map

.ped file contains info on the individual genotypes
```
head -1 Results/hapmap-ceu.ped
```

###Import VCF into plink A VCF (Variant Call Format) file is a standard file format used in bioinformatics to store genetic variation data, such as single nucleotide polymorphisms (SNPs) and insertions/deletions (indels), typically obtained from DNA sequencing. It contains information about the genomic location, alleles, genotype, and quality score of each variant called.

./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

We can select individuals based on the completness of their genotype


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

Select specific markers

In this way we select only a specific marker, in this case SNP rs9930506

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

Merge genetic files

We can merge different files (different set of individuals, in this case)

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

Add a phenotype into PLINK files

PLINK file can also store info on a phenotype



head Data/1kg_EU_qc.fam


head Data/1kg_EU_qc.bim

This file contains info on BMI of different individuals


head Data/BMI_pheno.txt

This is how we add a phenotipic information to a plink file

./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

We can calculate 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