UKBioBank Helper Modulefile

Overview

These modulefiles set only environment variables to make accessing the centrally hosted UK Bio Bank Full Release Datasets easier on the CSF. They allow you to use the environment variables in your jobscripts to access the correct folders that provide the central copy of the UK Bio Bank data.

The information on this webpage is also valid for the iCSF

Restrictions on use

To access the UK Bio Bank data on the CSF you must be added to a group on the system that has the correct access permissions (the dataset-ukbiobank-full Unix group). To be added to this group please email its-ri-team@manchester.ac.uk with confirmation of your approved UKBioBank/EGA access to the data – the UKBioBank have advised us that supplying us with a copy of your Material Transfer Agreement (MTA) is suitable proof of access (please remove any passwords from your documentation). If you are sending a screenshot of the BioBank Portal which shows who is named on the MTA, please also include a screenshot (if possible) showing which datasets your project is permitted to use.

For details on registering with the UK Bio Bank / European Genome Archive please see the UK BioBank Full Release FAQ (hosted by the UK Bio Bank).

Set up procedure

Access to the UKBioBank corrected v3 dataset

In 2018 the UKBioBank released v3 of the imputed dataset to correct some mistakes in the v2 dataset. New users should use this corrected version. Please load the modulefile:

# Access to the corrected v3 imputed dataset EGAD00010001474 and genotype dataset EGAD00010001497

module load tools/env/ukbiobank-full-release-2018

Access to the UKBioBank incorrect v2 dataset

The original modulefile providing access to the incorrect v2 imputed dataset EGAD00010001225 is still available. This is because you may have been using particular files in that study that the UKBioBank did not need to correct or you may be using the genotyped data in study id EGAD00010001226, which contains entirely correct data,

# Access to the incorrect v2 imputed dataset EGAD00010001225 and genotyped dataset EGAD00010001226

module load tools/env/ukbiobank-full-release      # New user should NOT use this modulefile

Environment variables

The new 2018 modulefile sets the following environment variables (items in bold have changed since the previous modulefile):

# Settings provided by the tools/env/ukbiobank-full-release-2018 modulefile:

UKBIOBANK_BASE            =   /mnt/data-sets/ukbiobank/full-release
UKBB_BASE                 =   /mnt/data-sets/ukbiobank/full-release

# This is the new, correct, v3 imputation data (March 2018)
UKBB_IMPUTATION_STUDYID   =   EGAD00010001474

# This is identical to the EGAD00010001226 data
UKBB_GENOTYPED_STUDYID    =   EGAD00010001497

# NB: No trailing 001 subdirectory
UKBB_IMPUTATION_DIR       =   /mnt/data-sets/ukbiobank/full-release/EGAD00010001474

# Symlink / shortcut to EGAD00010001226/001
UKBB_GENOTYPED_DIR        =   /mnt/data-sets/ukbiobank/full-release/EGAD00010001497

# Includes names of v3 (correct) imputed data files
UKBB_FILELIST             =   /mnt/data-sets/ukbiobank/full-release/filelist.2018.txt

The original modulefile makes the following settings (please be cautious – do you really need to access these datasets?):

# Settings provided by the tools/env/ukbiobank-full-release modulefile:
# USE WITH CAUTION - NEW USERS SHOULD USE THE ABOVE MODULEFILE, NOT THIS ONE!

UKBIOBANK_BASE            =   /mnt/data-sets/ukbiobank/full-release
UKBB_BASE                 =   /mnt/data-sets/ukbiobank/full-release

# This dataset should NOT be used (March 2018)
UKBB_IMPUTATION_STUDYID   =   EGAD00010001225

# This dataset can be used (it is identical to EGAD00010001497)
UKBB_GENOTYPED_STUDYID    =   EGAD00010001226

UKBB_IMPUTATION_DIR       =   /mnt/data-sets/ukbiobank/full-release/EGAD00010001225/001
UKBB_GENOTYPED_DIR        =   /mnt/data-sets/ukbiobank/full-release/EGAD00010001226/001

# Includes names of v2 (incorrect) imputed data files
UKBB_FILELIST             =   /mnt/data-sets/ukbiobank/full-release/filelist.txt

Basic Usage of Environment Variables

You can use any of the above environment variables in your jobscripts and other commands. The following examples assume you have first done:

module load tools/env/ukbiobank-full-release-2018

For example, to see all of the files in the GENOTYPED dataset:

ls -lh $UKBB_GENOTYPED_DIR

# Note: The compressed .gz files and checksum .md5 files
#       will also be listed.

To use the variables in a jobscript, load the modulefile (either on the login node or in the jobscript) and then you can use the variables to access particular files. For example:

MyGenomeApp -input $UKBB_GENOTYPED_DIR/ukb_cal_chr16_v2.bed -o myresults.dat

Job Arrays

The text file given by the $UKBB_FILELIST variable contains a list of the datasets available:

cat $UKBB_FILELIST
EGAD00010001474/ukb_imp_chr1_v3.bgen              # Note the v3 imputed files have changed their names compared to the v2 files
EGAD00010001474/ukb_imp_chr2_v3.bgen
EGAD00010001474/ukb_imp_chr3_v3.bgen
...
EGAD00010001474/ukb_mfi_chrX_v3.txt
EGAD00010001474/ukb_mfi_chrXY_v3.txt
...
EGAD00010001497/ukb_l2r_chrXY_v2.txt
EGAD00010001497/ukb_l2r_chrY_v2.txt
   #
   # Notice that the subdirectories EGAD00010001474 and EGAD00010001497 are included in the name

You may use this file when running job arrays on the CSF to process all files in a particular dataset. For example:

Suppose we wish to process all of the ukb_int_chrN_v2.bin files in the EGAD00010001497 study (this is the same dataset as the EGAD00010001226 study hence still use v2 in their name).

  1. Load the modulefile on the login node: 
    module load tools/env/ukbiobank-full-release-2018
  2. Check which files we will be processing: 
    grep ukb_int_chr $UKBB_FILELIST
  #
  # 'grep' prints all lines that contain the string 'ukb_int_chr'

EGAD00010001497/ukb_int_chr1_v2.bin
EGAD00010001497/ukb_int_chr2_v2.bin
...
EGAD00010001497/ukb_int_chrY_v2.bin
   #
   # Notice that the subdirectory EGAD00010001497/ is included in the name
  3. Count the number of files and hence number of tasks needed in the job array (you probably expect this to be 26 but let’s check!) 
    grep ukb_int_chr $UKBB_FILELIST | wc -l 
                                  #
                                  # 'wc' is a word count utility (-l counts lines) 26
  4. Write a job array script that will automatically run 26 copies (‘tasks’) of the job where each ‘task’ is given a unique ID 1, 2, …, 26. We will use this to make each task process a different dataset (one of the 26 files listed above): 
    #!/bin/bash --login
#$ -cwd                # Run in current directory
#$ -t 1-26             # Run a 26-task job array
### No -V line (we load the modulefile in the jobscript, hence added --login above)

### Load the modulefiles in the jobscript
module load tools/env/ukbiobank-full-release-2018

### You will probably want to load modulefiles for bio-inf applications
module load name/of/my/app/1.2.3

### $SGE_TASK_ID is set to 1, 2, ... 26 (one for each of the 26 tasks)
### Read the N-th filename by generating the list as we did earlier
FILENAME=`grep ukb_int_chr $UKBB_FILELIST | awk "NR==$SGE_TASK_ID {print}"`

### Report what we are doing
echo "Processing $UKBB_BASE/$FILENAME in job array $JOB_ID task $SGE_TASK_ID"

### Process the file for this task (change this to use your own real app here!)
myGenomeApp -input $UKBB_BASE/$FILENAME -output myResult_$SGE_TASK_ID.data
  5. Submit the job once using the usual command: 
    qsub myjobscript

    where myjobscript is the name of your jobscript file.

Further Dataset Format Information

For a description of the datasets, a text file provided by the UK Bio Bank is available using:

less $UKBB_BASE/ukb_genetic_file_description.txt

This file is also available online (hosted by the UK Bio Bank).

Further info

Updates

None.

Last modified on July 27, 2022 at 10:28 am by George Leaver