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
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
22. LD-based results clumping
23. Gene-based report
25. Rare CNVs
26. Common CNPs
28. Annotation web-lookup
29. Simulation tools
30. Profile scoring
31. ID helper
35. FAQ & Hints
Version 1.07 released 10 October 2009
This release contains a number of major new features:
A full list of changes is detailed in the CHANGELOG.
- 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
Version 1.06 released 22 April 2009
This release contain a number of minor improvements and bug-fixes as well as some major enhancements:
A full list of changes is detailed in the CHANGELOG.
- 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
Version 1.05 released 11 December 2008
This release contains a number of additional features, format changes
and bug fixes, including:
There is now a flow-chart that details the order of major operations in PLINK.
For the full list of changes, see the CHANGELOG.
- 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)
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
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:
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
- 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.
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