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

Warnings & Known Issues

Development of PLINK is ongoing: as such, there is always likely to be a list of features that are only partialy implemented, or have problems of some kind. Our policy is to release a web-based warning for these as soon as any problems are identified, and, for more major problems, to release a patched version on the main download page as soon as possible.

Note that any new patched verions will still give the web-based warning message (i.e. that is based solely on version number, rather than patch).

Want to ignore a warning and run the analysis anyway? Then run PLINK with the --noweb flag to disable the web-check. Not recommended...

Often, the issues flagged here are fixed in the development source code, available from , which you will need to compile yourself.

Format issue with --hardy option

Date: Sep 1 2008

Version: 1.04

Problem: The output of the --hardy command has the fields in the wrong order, with the TEST and A1, A2 fields swapped. Also, the A2 field always equal the A1. This is fixed in development source code available online; will be fixed in next release

Problem with --chap and missing genotype data

Date: Oct 20 2008

Version: 1.04

Problem: A serious problem emerged with the conditional haplotype tests: when there is a reasonable amount of missing genotype data, the p-values calculated can be very liberal. This is because individuals were included under the null model likelihood calculations but not the alternate model calculations under these scenarios. Fixed in development source code; will be fixed in next release. As an approximate, temporary fix, add the option --hap-miss 2 (this will mean that all individuals are phased and included in the test, no matter how much missing genotype data they have)

This document last modified Wednesday, 25-Jan-2017 11:39:28 EST