PLINK: Whole genome data analysis toolset plink...
Latest PLINK release is v1.07 (10-Oct-2009)

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
 

Credits

PLINK is developed by Shaun Purcell, with the help of others.

In particular, Douglas Ruderfer has contributed to many internal functions and has performed extensive testing.

Below is a list of others who have been involved in one way or another:
  • Paul de Bakker: testing and many detailed suggestions
  • David Bender: Haploview interface for veiwing PLINK results
  • Mark Daly: various statistical and computational algorithms
  • Julian Maller: Haploview interface for veiwing PLINK results
  • Ben Neale: IBD estimation routines
  • Robert Plenge: early beta-testing
  • Lori Thomas: development of PLINK-O-MATIC and beta version of gPLINK
  • Kathe Todd-Brown: gPLINK development
  • Pak Sham: IBD estimation and other association routines
and others at MGH, the Broad Institute and elsewhere. Thanks!

 
This document last modified Friday, 09-Oct-2009 18:58:20 EDT