17 Oct 2014 | Christopher C Chang, Carson C Chow, Laurent CAM Tellier, Shashaank Vattikuti, Shaun M Purcell, James J Lee
PLINK 1.9 introduces significant performance improvements and scalability enhancements for genome-wide association studies (GWAS) and population genetics research. Key advancements include extensive use of bit-level parallelism, $O(\sqrt{n})$-time/constant-space Hardy-Weinberg equilibrium and Fisher's exact tests, and other algorithmic optimizations. These changes accelerate operations by 1-4 orders of magnitude and enable handling of datasets larger than available RAM. PLINK 2.0 will introduce a new data format capable of representing probabilities, phase information, and multiallelic variants, along with extensions to existing functions to accommodate these new types of data. The improvements aim to address the challenges posed by larger and richer datasets, making PLINK more versatile and efficient for modern genetic studies.PLINK 1.9 introduces significant performance improvements and scalability enhancements for genome-wide association studies (GWAS) and population genetics research. Key advancements include extensive use of bit-level parallelism, $O(\sqrt{n})$-time/constant-space Hardy-Weinberg equilibrium and Fisher's exact tests, and other algorithmic optimizations. These changes accelerate operations by 1-4 orders of magnitude and enable handling of datasets larger than available RAM. PLINK 2.0 will introduce a new data format capable of representing probabilities, phase information, and multiallelic variants, along with extensions to existing functions to accommodate these new types of data. The improvements aim to address the challenges posed by larger and richer datasets, making PLINK more versatile and efficient for modern genetic studies.