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

Dataset type: Software
Data released on February 23, 2015

Chang CC; Chow CC; Lee JJ; Purcell SM; Tellier LCAM; Vattikuti S (2015): Software and supporting material for "Second-generation PLINK: rising to the challenge of larger and richer datasets". GigaScience Database.


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.
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.
Most pipelines currently employing PLINK 1.07 can expect to benefit from upgrading.
For the most recent updates please visit the project home page and GitHub repository.

Additional details

Read the peer-reviewed publication(s):

Chang, C. C., Chow, C. C., Tellier, L. C., Vattikuti, S., Purcell, S. M., & Lee, J. J. (2015). Second-generation PLINK: rising to the challenge of larger and richer datasets. GigaScience, 4(1). doi:10.1186/s13742-015-0047-8

Additional information:

File NameSample IDData TypeFile FormatSizeRelease Date 
Sequence variantsTAR28.88 MB2015-01-23
Sequence variantsTAR93.1 MB2015-01-23
Sequence variantsTAR27.41 MB2015-01-23
Sequence variantsTAR17.23 MB2015-01-23
Sequence variantsTAR17.36 MB2015-01-23
Sequence variantsTAR101.54 MB2015-01-23
Sequence variantsTAR83.75 MB2015-01-23
Sequence variantsTAR84.22 MB2015-01-23
Sequence variantsTAR77.21 MB2015-01-23
Sequence variantsTAR76.1 MB2015-01-23
Displaying 11-20 of 31 File(s).
Date Action
April 27, 2015 Manuscript Link added : 10.1186/s13742-015-0047-8
November 2, 2015 File 1kg_phase1_all.tar.gz updated