Second-generation PLINK: Rising to the challenge of larger and richer datasets

Christopher C. Chang, Carson C. Chow, Laurent C.A.M. Tellier, Shashaank Vattikuti, Shaun M. Purcell, James J. Lee

Research output: Contribution to journalArticlepeer-review

2103 Scopus citations


Background: PLINK 1 is a widely used open-source C/C++ toolset for genome-wide association studies (GWAS) and research in population genetics. However, the steady accumulation of data from imputation and whole-genome sequencing studies has exposed a strong need for faster and scalable implementations of key functions, such as logistic regression, linkage disequilibrium estimation, and genomic distance evaluation. In addition, GWAS and population-genetic data now frequently contain genotype likelihoods, phase information, and/or multiallelic variants, none of which can be represented by PLINK 1's primary data format. Findings: To address these issues, we are developing a second-generation codebase for PLINK. The first major release from this codebase, PLINK 1.9, introduces extensive use of bit-level parallelism, O(√n)-time/constant-space Hardy-Weinberg equilibrium and Fisher's exact tests, and many other algorithmic improvements. In combination, these changes accelerate most operations by 1-4 orders of magnitude, and allow the program to handle datasets too large to fit in RAM. We have also developed an extension to the data format which adds low-overhead support for genotype likelihoods, phase, multiallelic variants, and reference vs. alternate alleles, which is the basis of our planned second release (PLINK 2.0). Conclusions: The second-generation versions of PLINK will offer dramatic improvements in performance and compatibility. For the first time, users without access to high-end computing resources can perform several essential analyses of the feature-rich and very large genetic datasets coming into use.

Original languageEnglish (US)
Article number7
Issue number1
StatePublished - Feb 25 2015

Bibliographical note

Publisher Copyright:
© 2015 Chang et al.; licensee BioMed Central.


  • Computational statistics
  • GWAS
  • High-density SNP genotyping
  • Population genetics
  • Whole-genome sequencing

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