Written by Busisiwe Mlotshwa June 23, 2016
The focus of PLINK is purely on analysis of genotype/phenotype data. using PLINK, researchers can read data in a variety of formats, recode and reorder files, merge two or more files, extract subsets (SNPs or individuals), flip strand of SNPs and compress data in a binary file format. PLINK also enables researchers to perform summary statistics for quality control, detect population stratification, perform basic association testing, predict multimarkers and haplotypic tests, perform copy number variant analysis and meta-analyses, among a range of other functions. PLINK is easy to use and compatible with a host of other software if additional downstream analyses are desired.
Copied from the PLINK website: PLINK is a free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale genotype/ phenotype analyses in a computationally efficient manner