Computer Exercises
Workshop on Methods for Genome-wide Association Studies
25th May 2017
The Chinese
University of Hong Kong
The lecture slides are available here: HongKongGWAS.pdf
Software Required
To participate in the computer exercises you will need to download several pieces of software. I recommend that you try downloading these and getting them running before the workshop. If you are using a Windows computer, you will need to run the programs using the command line or MS-DOS prompt. Some useful instructions for doing this can be found at:http://www.computerhope.com/issues/chdos.htm
You will also need to download the following software to your computers:
PLINK:
If you are working on Windows (MS-DOS) you can hopefully just save the following file to an appropriate folder on your machine:plink.exe
[Right click, select Save Target As, and navigate through to save it in the desired folder].
Alternatively you can download PLINK version 1.07 from:
http://zzz.bwh.harvard.edu/plink/download.shtml
(Note that we will be using the command-line version, not the gPLINK GUI).
Or else you can download the newer version, PLINK 1.90, from:
https://www.cog-genomics.org/plink/1.9/
FaST-LMM:
You will also need to get FaST-LMM running on your computer in order to do the last exercise. If you are working on Windows (MS-DOS) you can hopefully just save the following files to an appropriate folder on your machine:FastLmmC.exe
libiomp5md.dll
[Right click, select Save Target As, and navigate through to save it in the desired folder].
Alternatively, FaST-LMM can be obtained from:
http://research.microsoft.com/en-us/downloads/aa90ccfb-b2a8-4872-ba00-32419913ca14/
R:
You will also need to get R running on your computer in order to visualise the results of your analyses. R can be obtained from:http://www.r-project.org/
Computer Exercises: