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
 

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
        URL:         http://pngu.mgh.harvard.edu/purcell/plink/

        Purcell S, Neale B, Todd-Brown K, Thomas L, 
        Ferreira MAR, Bender D, Maller J, de Bakker PIW, 
        Daly MJ & Sham PC (in press) PLINK: a toolset 
        for whole-genome association and population-based 
	linkage analysis. American Journal of Human Genetics.
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 11:39:26 EST