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Getting the software

In this tutorial we will use two pieces of software designed for GWAS analysis:

  • plink 1.9 'beta', which is a general-purpose tool for manipulating genome-wide data
  • gcta which implements (amongst other thins) a linear mixed model for association analysis.

We will also R to make plots and (for one step) we'll write an exciting python script!

To make things as easy as possible, we have included both plink and gcta in the data tarball.

Look in the software folder and pick the relevant version for your platform.

Windows note

Windows users should work in the Ubuntu for Windows system, and use the linux version.

For this tutorial we recommend copying the relevant versions into the top-level gwas_tutorial folder

cp software/[version]/plink ./
cp software/[version]/gcta64 ./

You can then test the software out:

./plink
./gcta64
Mac firewall note

On a mac, you may need to allow access to this software using System Preferences. This lives in System Preferences -> Privacy and Security -> scroll down to 'Security' pane. After you have tried to run the software once, you should see a box like this:

img

If you give permission, you're able to run the software on subsequent attempts.

If all works out, you should now see a message like:

$ ./plink
PLINK v1.9.0-b.7.7 64-bit (22 Oct 2024)            cog-genomics.org/plink/1.9/
(C) 2005-2024 Shaun Purcell, Christopher Chang   GNU General Public License v3

  plink <input flag(s)...> [command flag(s)...] [other flag(s)...]
  plink --help [flag name(s)...]

Commands include --make-bed, --recode, --flip-scan, --merge-list,
--write-snplist, --list-duplicate-vars, --freqx, --missing, --test-mishap,
--hardy, --mendel, --ibc, --impute-sex, --indep-pairphase, --r2, --show-tags,
--blocks, --distance, --genome, --homozyg, --make-rel, --make-grm-gz,
--rel-cutoff, --cluster, --pca, --neighbour, --ibs-test, --regress-distance,
--model, --bd, --gxe, --logistic, --dosage, --lasso, --test-missing,
--make-perm-pheno, --tdt, --qfam, --annotate, --clump, --gene-report,
--meta-analysis, --epistasis, --fast-epistasis, and --score.

"plink --help | more" describes all functions (warning: long).

and

$ ./gcta64
*******************************************************************
* Genome-wide Complex Trait Analysis (GCTA)
* version v1.94.1 Mac
* (C) 2010-present, Yang Lab, Westlake University
* Please report bugs to Jian Yang <jian.yang@westlake.edu.cn>
*******************************************************************
Analysis started at 09:46:46 GMT on Wed Nov 06 2024.
Hostname: dhcp570.well.ox.ac.uk

Error: no analysis has been launched by the option(s)
Please see online documentation at https://yanglab.westlake.edu.cn/software/gcta/

Congratulations! You're ready to start the tutorial.