PLINK: Whole genome data analysis toolset

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
e:

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 hapmap1.zip 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:
dir

which should show 4 new files in addition to the zip archive:
     E:\example>dir
      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 hapmap1.map
     06/05/2006  10:24 PM        29,739,617 hapmap1.ped
     06/05/2006  08:29 PM         2,913,399 hapmap1.zip
     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:
erase hapmap1.zip

You are now ready to return to the main tutorial.
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