Software and supporting material for "Second-generation PLINK: rising to the challenge of larger and richer datasets".

Because of its broad functionality and efficient binary file format, PLINK is widely employed in data-processing pipelines set up for gene-trait mapping and populationgenetic studies. The five years since the final first-generation update (v1.07), however, have witnessed the introduction of new algorithms and analytical approaches, the growth in size of typical datasets, and wide deployment of heavily multicore processors.<br>
In response, we have developed PLINK 1.9, a comprehensive performance, scaling, and usability update. Our data indicate that its speedups frequently exceed two, and sometimes even three, orders of magnitude for several commonly used operations. Its core functional domains are unchanged from that of its predecessor data manage-ment, summary statistics, population stratification, association analysis, identity by descent estimation and it is usable as a drop-in replacement in most cases, requiring no changes to existing scripts.<br>
Most pipelines currently employing PLINK 1.07 can expect to benefit from upgrading.<br>
For the most recent updates please visit the project home page and GitHub repository.