Editing UK Biobank/Downloading the data

These procedures were all derived from the [http://biobank.ctsu.ox.ac.uk/showcase/exinfo.cgi?src=accessing_data_guide documentation] at the UK Biobank. This information is here as a record and reference. Researchers should not have to repeat these steps.

== 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>

== Genotypic data ==
<ol>
<li> Genetic data is downloaded following the instructions at [http://biobank.ctsu.ox.ac.uk/showcase/exinfo.cgi?src=AccessingGeneticData the UK Biobank site].
<li> Scripted downloads of all chromosomes were done using a command such as
<syntaxhighlight lang="bash">
$ seq 1 26 | parallel -j1 ./gfetch cal {}
$ seq 1 26 | parallel -j1 ./gfetch imp {}
</syntaxhighlight>
<li> A single sample map (impv1.sample) for the imputed data also was downloaded
<syntaxhighlight lang="bash">
$ ./gfetch imp 1 -m
</syntaxhighlight>
</ol>

== Quality Control ==
<ol>
We identified lists of individuals and positions to exclude from information in the UKB data and in the Axiom Array unimputed genotypes.
<li> All files can be found on RC at: /work/KellerLab/UKBiobank/genetics/raw/Quality_Control
<li> UKB and Affymetrix performed a number of QC analyses to exclude questionable positions and identify individual samples. Additional pdfs from the UKBiobank are found within /work/KellerLab/UKBiobank/genetics/raw/Quality_Control/UK_Biobank_Axiom_Array
<li> Additional Affymetrix and UKB information can be found on their websites:
        [http://www.ukbiobank.ac.uk/scientists-3/uk-biobank-axiom-array/ UK Biobank Axiom Array], [https://www.jiscmail.ac.uk/cgi-bin/webadmin?A0=UKB-GENETICS UKB-Genetics Archive]
<li> A list of 1068 individuals to exclude is in Exclude_individuals.poorQC.UKB_Affy_sex.id on RC.
<li> A list of 8010 positions to exclude is in duplicate.positions.excludesnps.txt on RC.
<li> A README.txt file located on RC contains the steps used and additional information.