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

What's new?

Version 1.07 released 10 October 2009

This release contains a number of major new features:
  • Meta-analysis of generic association test summary data | link
  • Analysis of post-imputation dosage data | link
  • Result file annotation functions | link
  • Preliminary support for ZLIB file compression, which will be extended to all operations in future releases
A full list of changes is detailed in the CHANGELOG.

Version 1.06 released 22 April 2009

This release contain a number of minor improvements and bug-fixes as well as some major enhancements:
  • Haplotype block estimation and SNP tagging features | link
  • Covariates and permutation allowed for haplotype-based tests | link
  • Extensive ID-helper utility functions | link
  • Support for LAPACK library, to speed up MDS analysis | link
  • Additional input format features for long-format files | link
  • Attributes for filtering SNPs and individuals | link
A full list of changes is detailed in the CHANGELOG.

Version 1.05 released 11 December 2008

This release contains a number of additional features, format changes and bug fixes, including:
  • More flexible support for R-plugins (note: protocol changed for R functions, see R plugin page for details)
  • Preliminary support for quality scores (SNPs and genotypes)
  • Calculation of expected IBD sharing for known relatives
  • Various commands to update individual and SNP information
  • Many minor fixes and changes (including to some output files)
There is now a flow-chart that details the order of major operations in PLINK. For the full list of changes, see the CHANGELOG.

Version 1.04 released 26 August 2008

This release contains a number of additional features. There is a new set-based test, various commands for parsing SNP and CNV data and results by genes. There are also a number of smaller new features and bug fixes, described in the CHANGELOG. A new PDF snapshot of the online documentation has also been created.

Version 1.03 released 10 June 2008

A number of minor additions and bug fixes, described here

Version 1.02 released 27 March 2008

This version contains a whole new suite of tools for handling copy number variation data, for both rare (segmental) and common variants. As well as a number of minor fixes and improvements, the web manual is now available as a single PDF file.

Version 1.01 released 27 January 2008

This contains a number of additions and fixes, largely minor in nature, relative to 1.00. In particular, there is updated proxy association/imputation command syntax, output, features and default settings. Problems introduced in the last release, in QFAM, sliding window haplotype analysis, and the --hap-impute function are fixed. Also, some convenience functions have been added, e.g. to update a map file (--update-map) and create dummy variables for categorical covariates (--dummy-coding). In addition, various parts of the online documentation have been updated.

Version 1.00 released 5 December 2007

After a relatively long period since 0.99s was released, version 1.00, the first "stable" release, provides several important fixes and updates as well as several completely new features. Although several new features are designated as being in a beta stage of development, releasing as version 1.00 (as opposed to 0.99t) signifies both a reasonable level of maturity for many parts of this package as well as the fact that PLINK will, for the foreseeable future, still be subject to regular change (in the form of additions and updates as well as bug fixes).

The main new features are

Version 0.99s released 27 July 2007

There are several entirely new sets of features in version v0.99s. This release was scheduled to be the v1.00 release, but given the number of new features added, it seemed appropriate to have one more beta release, to iron out any major problems before the main release.

The main additions are:
  • A set of proxy association methods, that are designed to present single SNP associations in their haplotypic context: for example, is a single SNP association also seen in the surrounding haplotypes? Also, the basic single SNP test is reframed in terms of a haplotype test, which can have some advantages with respect to non-random genotyping failure.
  • There is now a web-based lookup function, to quickly give report a set of different types of annotation data for particular SNPs.
  • PLINK now has some degree of extensibility, via a R plugin feature. Users can define their own test statistic using the R language, which can then be easily embedded within a PLINK run.
  • Data can now be loaded in "long format" (in which one row corresponds to a genotype, rather than a person or a SNP).
  • Changed the implementation of the --homozyg-* functions, that looks for extended stretches of homozygosity.
  • Several other minor additions and bug-fixes. Most notable bug fixes are for the DFAM test, having covariates and genotypic tests in the --linear and --logistic functions; a problem with the --bmerge option.
There have also been a number of improvements and fixes made to the gPLINK GUI (now version v1.00). In addition, several improvements and additions relevant to viewing PLINK output files have been made to the Haploview program (version 4.0, release candidate 2) available from here.

Version 0.99r released 29 April 2007

Main additions include the DFAM and QFAM tests, in addition to several bug fixes and data management options.

Manuscript describing PLINK in press

A manuscript is in press (American Journal of Human Genetics). Please do not distribute this pre-publication version.

This document last modified Wednesday, 25-Jan-2017 11:39:27 EST