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

A PLINK tutorial

These notes are designed to help Windows users who are unfamiliar with the command line to set up the example files for the tutorial.

Go to the start menu and select the "Run..." option

Type "cmd" at the prompt.

This should bring up a command window (i.e. this is MS-DOS). Using the command line, create a new folder for the tutorial files. In this case, I've first moved to the drive called "E" by typing

You might not have a drive called E: -- your default drive is probably C:. The exact location of where you run this tutorial is not important -- we are next going to create a folder, but this can be anywhere on your system.

By typing (all on one line)
mkdir example

we have created a new folder called example (assuming this did not already exist). Move into this new folder with the cd command: (all on one line)
cd example

Finally, using Windows, copy the file you downloaded to this folder and unzip, e.g. using WinZip as below. If you do not have WinZip installed, you can obtain a free evaluation copy from the product's website


You now should return to the command line prompt, which will still be point to the newly created directory, with the required PED and MAP files in it. You can verify this by typing at the command line:

which should show 4 new files in addition to the zip archive:
      Volume in drive E is New Volume
      Volume Serial Number is XXXX-XXXX

      Directory of E:\example

     06/05/2006  08:36 PM    <DIR>          .
     06/05/2006  08:36 PM    <DIR>          ..
     06/05/2006  11:24 PM         1,693,668
     06/05/2006  10:24 PM        29,739,617 hapmap1.ped
     06/05/2006  08:29 PM         2,913,399
     06/05/2006  11:24 PM            93,968 pop.phe
     06/05/2006  11:24 PM            93,968 qt.phe

                    3 File(s)     34,346,684 bytes
                    2 Dir(s)  34,455,240,704 bytes free
You can erase the ZIP file with this command:

You are now ready to return to the main tutorial.

This document last modified Wednesday, 25-Jan-2017 11:39:26 EST