uk_biobank:downloading_the_data
Table of Contents
These procedures were all derived from the documentation at the UK Biobank. This information is here as a record and reference. Researchers should not have to repeat these steps.
Phenotypic data
- The phenotype file was downloaded from UK Biobank by the project PI as instructed in the data accessibility email.
- All of the utilities from the UK Biobank download page were retrieved.
- The key, k1234.key was saved from the PI's email.
- This command was run to decrypt the downloaded phenotype file
$ ./ukb_unpack ukb1234.enc k1234.key
which produced the file ukb1234.enc_ukb
- Once decrypted, the following commands were run to extract the data into useful formats
$ ./ukb_conv ukb1234.enc_ukb bulk -eencoding.ukb $ ./ukb_conv ukb1234.enc_ukb docs -eencoding.ukb $ ./ukb_conv ukb1234.enc_ukb r -eencoding.ukb
- bulk is a list of IDs for use with the ukbfetch utility
- docs produces an html file containing documentation of the variables in this dataset
- r produces a tab deliminated file and an R script for labeling and putting levels on the variables.
Genotypic data
- Genetic data is downloaded following the instructions at the UK Biobank site.
- Scripted downloads of all chromosomes were done using a command such as
$ seq 1 26 | parallel -j1 ./gfetch cal {} $ seq 1 26 | parallel -j1 ./gfetch imp {}
- A single sample map (impv1.sample) for the imputed data also was downloaded
$ ./gfetch imp 1 -m
Quality Control
We identified lists of individuals and positions to exclude from information in the UKB data and in the Axiom Array unimputed genotypes.
- A very brief overveiw of QC steps can be found in this .pptx file2020_04_22_ukb_qc.pptx.
- All files can be found on RC at: /work/KellerLab/UKBiobank/genetics/raw/Quality_Control
- 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
- Additional Affymetrix and UKB information can be found on their websites:
UK Biobank Axiom Array, UKB-Genetics Archive
- A list of 1068 individuals to exclude is in Exclude_individuals.poorQC.UKB_Affy_sex.id on RC.
- A list of 8010 positions to exclude is in duplicate.positions.excludesnps.txt on RC.
- A README.txt file located on RC contains the steps used and additional information.
uk_biobank/downloading_the_data.txt · Last modified: by luev6784