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

Getting started with PLINK

This page contains some important information on learning to use PLINK and how to handle any problems you encounter.

We suggest that after downloading PLINK you first try the tutorial. This will familiarize you with the basic PLINK commands.

Citing PLINK

If you use PLINK in any published work, please cite both the software (as an electronic resource/URL) and the manuscript describing the methods.
        Package:     PLINK (including version number)
        Author:      Shaun Purcell

        Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MAR, 
	Bender D, Maller J, Sklar P, de Bakker PIW, Daly MJ & Sham PC (2007) 
        PLINK: a toolset for whole-genome association and population-based 
	linkage analysis. American Journal of Human Genetics, 81.

Reporting problems, bugs and questions

If you have any problems with PLINK or would like to report a bug, please follow these steps:


When an analysis does not report the results you expect, or when PLINK seemingly gives different answers to previous versions or to other software packages, or the last time you ran it, etc, please feel me to e-mail me
     plink AT chgr DOT mgh DOT harvard DOT edu
but also please consider the following before doing so:

  1. Please first check the Frequently Asked Questions list to see if your question has already been answered

  2. Please check the LOG file, it often contains important information. For example, did it filter out some individuals based on genotyping rate or missing phenotype/sex information which you were not expecting?

  3. Please check the format of your data: is it plain text? does each file have the correct number of rows, etc. Are the missing value codes appropriate?

  4. Please recheck the web-documentation: sometimes the syntax of an option may change.

  5. If the above steps do not resolve your problem, then please e-mail me plink AT chgr dot mgh dot harvard dot edu (this is different from the mailing list -- i.e. your e-mail will only be sent to me, not the whole list). The more specific your e-mail, the easier it will be for me to diagnose any problem or error. Please include:

    • The whole LOG file(s)

    • The type of machine you were using

    • Ideally, please try to make some reduced dataset that replicates the problem that you are able to send to me in a ZIP file, so that I will be able to recreate the problem; any data sent to me for these purposes will be immediately deleted after I have resolved the problem.

HINT The more of the above steps you follow, the more likely you are to receive a timely, useful response! If you haven't heard within a week or so, please feel free to send a reminder e-mail...

IMPORTANT I am willing and able to advise on the use of specific features implemented in PLINK: to diagnose whether they are working as intended and to give a generic description of a procedure or method, if it is unclear from the web documentation. I'm afraid I will not necessarily be able to give specific advice on any one particular dataset, why you should use one method over another, what it all means, etc...

This document last modified Thursday, 01-Oct-2009 08:00:57 EDT