PLINK: Whole genome data analysis toolset plink...
Last original PLINK release is v1.07 (10-Oct-2009); PLINK 1.9 is now available for beta-testing

Whole genome association analysis toolset

Introduction | Basics | Download | Reference | Formats | Data management | Summary stats | Filters | Stratification | IBS/IBD | Association | Family-based | Permutation | LD calcualtions | Haplotypes | Conditional tests | Proxy association | Imputation | Dosage data | Meta-analysis | Result annotation | Clumping | Gene Report | Epistasis | Rare CNVs | Common CNPs | R-plugins | SNP annotation | Simulation | Profiles | ID helper | Resources | Flow chart | Misc. | FAQ | gPLINK

1. Introduction

2. Basic information

3. Download and general notes

4. Command reference table

5. Basic usage/data formats 6. Data management

7. Summary stats 8. Inclusion thresholds 9. Population stratification 10. IBS/IBD estimation 11. Association 12. Family-based association 13. Permutation procedures 14. LD calculations 15. Multimarker tests 16. Conditional haplotype tests 17. Proxy association 18. Imputation (beta) 19. Dosage data 20. Meta-analysis 21. Annotation 22. LD-based results clumping 23. Gene-based report 24. Epistasis 25. Rare CNVs 26. Common CNPs 27. R-plugins 28. Annotation web-lookup 29. Simulation tools 30. Profile scoring 31. ID helper 32. Resources 33. Flow-chart 34. Miscellaneous 35. FAQ & Hints

36. gPLINK

PLINK 1.9 and 2.0

Development of the baseline PLINK toolset has resumed and beta testing for the next (1.90) release has now begun.

The new release, by Chris Chang and colleagues, is a complete rewrite of the original code and represents a very significant improvement in overall speed and functionality. Moving forward, these changes should enable PLINK to meet the demands of ever-larger genetic datasets.

For download and documentation:

New features include:

  • Very large speed improvements across the board. Basic data management operations tend to be at least 5x as fast; speedup factors for more CPU-intensive functions such as --blocks, --fast-epistasis, --genome, --indep-pairwise, and --r2 frequently exceed 100x on multicore systems.
  • The new O(sqrt(n))-time implementations of SNP-HWE and Fisher's exact test can easily be adapted for inclusion in other software, and may be of particular interest to other tool developers.
  • Improved memory efficiency.
  • Conveniences such as direct VCF import/export and improved command-line help.

Questions, comments, and bug reports should now be directed to the plink2-users Google group:

The original version of PLINK will continue to be available for download at the original website.

PLINK 1.9 is currently under heavy active development -- users may wish to check certain results against the original PLINK (1.07) and notify the above list of any discrepancies.

This document last modified Thursday, 27-Oct-2011 15:43:46 EDT OA