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Getting set up

To run this practical you need two things: the software and the data.

Getting the software​

We will be using the software PLINK written by Christopher Chang: https://www.cog-genomics.org/). Before we start, please make sure you have downloaded this software and can run it in a terminal window on your system. To check this, try running this in your terminal window:

plink

You should see something like this:

PLINK v1.90b6.17 64-bit (28 Apr 2020)          www.cog-genomics.org/plink/1.9/
(C) 2005-2020 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, [...]

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

Getting the data​

The data files for this practical can be found in this folder.

Please download these now. For the first part of the practical we will use the chr19-clean.vcf.gz file, and later on we will use the other files as well.

For the practical we recommend making a new empty folder to put these in. So when you're ready to go your folder should look something like this:

PCA_practical/
    chr19-clean.vcf.gz
    merged.with.1000G.vcf.gz
    resources/
        1000GP_Phase3.sample

Make sure you are working in the above folder - you will need both a terminal and an R session. In the terminal:

cd /path/to/PCA_practical

In your R/RStudio session:

In R/RStudio:

setwd( '/path/to/PCA_practical' )

Next steps​

When you have the data, go and read the practical overview.