What is PLINK?
PLINK is an open-source toolset designed for whole-genome association studies (GWAS) and population-based linkage analysis. It is highly efficient for handling large-scale genotype data, particularly single nucleotide polymorphism (SNP) data from microarrays or sequencing.
Key Functions of PLINK
PLINK allows users to perform quality control, basic association testing, population stratification, linkage disequilibrium (LD) analysis, and more. You can filter out low-quality SNPs, individuals with missing data, or variants with low minor allele frequency (MAF) using simple command-line options.
Why Use PLINK?
PLINK is fast, flexible, and optimized for big genetic datasets. Researchers use it to find SNPs associated with diseases, traits, or drug responses. It also integrates well with other tools like R, Python, or genome browsers for downstream analysis and visualization.
Basic PLINK Workflow
A typical workflow involves converting raw genotype data (like .ped and .map or .vcf files) to binary format (.bed, .bim, .fam) for speed. After that, you can apply filters, perform association tests, and generate summary statistics—all with a few commands.
How to install plink to your system ?
- Install via this link
- Move the
plinkbinary to a directory in your PATH (e.g.,/usr/local/bin/) - Give it executable permission (just to be safe):
- Verify the installation via this command ( plink --version )
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