PLINKs

PLINKs commonly refer to the PLINK software family, a widely used toolkit for the analysis of genotype data in genome-wide association studies (GWAS). Developed to support quality control, basic statistics, and data management for large SNP datasets, PLINK is a cornerstone in many GWAS pipelines. The original PLINK was first released in 2007 and has since evolved into more scalable versions, with PLINK 2.0 introducing substantial performance improvements and expanded functionality.

Key features include support for common GWAS tasks such as quality control (filtering by call rate, Hardy-Weinberg equilibrium, minor allele frequency, sex checks, and relatedness), data management in standard formats (such as BED/BIM/FAM and PED/MAP), and a range of statistical tests. PLINK provides association tests for quantitative and binary traits (linear and logistic regression with covariates), as well as options for allele and genotype tests. It also offers tools for population structure assessment (e.g., principal components analysis), identity-by-descent estimation, and LD-based pruning and clumping to identify independent signals. Permutation testing and multiple-testing considerations are available in various forms, often in combination with downstream analyses.

PLINK outputs typically include summary statistics, sample and SNP quality metrics, and association results that are compatible with downstream visualization and interpretation tools. PLINK is free and open-source, cross-platform, and well-documented, making it a fundamental component of many genetic analysis workflows. The PLINK 2.0 lineage focuses on improved speed, memory efficiency, and broader input support (including VCF), while maintaining compatibility with established PLINK commands and workflows.