Editing UK Biobank/Downloading the data (section)

== Phenotypic data ==

<ol>
<li>The phenotype file was downloaded from UK Biobank by the project PI as instructed in the data accessibility email.</li>
<li>All of the utilities from the UK Biobank [http://biobank.ctsu.ox.ac.uk/showcase/download.cgi download] page were retrieved.</li>
<li>The key, k1234.key was saved from the PI's email.</li>
<li> This command was run to decrypt the downloaded phenotype file
<syntaxhighlight lang="bash">
$ ./ukb_unpack ukb1234.enc k1234.key
</syntaxhighlight>
which produced the file ukb1234.enc_ukb</li>
<li>Once decrypted, the following commands were run to extract the data into useful formats
<syntaxhighlight lang="bash">
$ ./ukb_conv ukb1234.enc_ukb bulk -eencoding.ukb
$ ./ukb_conv ukb1234.enc_ukb docs -eencoding.ukb
$ ./ukb_conv ukb1234.enc_ukb r -eencoding.ukb
</syntaxhighlight>
<ol>
<li>bulk is a list of IDs for use with the ukbfetch utility</li>
<li>docs produces an html file containing [https://ibg.colorado.edu/~lessem/ukb6395.html documentation of the variables] in this dataset</li>
<li>r produces a tab deliminated file and an R script for labeling and putting levels on the variables. 
</ol>
</li>
</ol>