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https://github.com/CirculatoryHealth/UKBioPick
The UKBioPick allows extraction of interested UK Biobank phenotypes.
https://github.com/CirculatoryHealth/UKBioPick
Last synced: 2 days ago
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The UKBioPick allows extraction of interested UK Biobank phenotypes.
- Host: GitHub
- URL: https://github.com/CirculatoryHealth/UKBioPick
- Owner: CirculatoryHealth
- License: mit
- Created: 2021-06-17T15:41:14.000Z (over 3 years ago)
- Default Branch: main
- Last Pushed: 2022-02-16T11:59:10.000Z (over 2 years ago)
- Last Synced: 2024-08-02T16:46:42.934Z (3 months ago)
- Language: Shell
- Size: 136 KB
- Stars: 2
- Watchers: 3
- Forks: 0
- Open Issues: 2
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
- awesome-uk-biobank - UKBioPick - delimited phenotypic file (ukbxxxx.tab) | (Data processing / Optical coherence tomography and fundus)
README
UKBioPick
============
[](LICENSE)
[](https://github.com/CirculatoryHealth/UKBioPick)
The UKBioPick allows extraction of interested UK Biobank (UKBB) phenotypes from tab-delimited phenotypic file (ukbxxxx.tab).
--------------
## Requirements
- `Bash`
- `Perl`
- UKBB phenotypic tab-delimited file (ukbxxxx.tab)
- Create a tab-separated file contains Field ID (column1) and Field (column2) (see example [_**here**_](data/Field_ID.txt). You can select Field ID and Field for each UKBB phenotypes in the [UKBB data dictionary Data_Dictionary_Showcase](https://biobank.ndph.ox.ac.uk/~bbdatan/Data_Dictionary_Showcase.csv).
## Usage
You must supply at least [4] arguments when running a UKBioPick!
Arguments | Description
--------------------------------- | --------------------------------
arg1 | UKBB phenotypic tab file (ukbxxxx.tab)
arg2 | Field ID and Field file
arg3 | Path to output directory
arg4 | Project name
You can run **UKBioPick** using the following command:
```
bash run_UKBioPick.sh [arg1:UKBB_phenotypics_tab_file] [arg2:field_ID_file] [arg3:output_directory] [arg4:project_name]
```
## Outputs
**UKBioPick** generates 2 output files:
- *_ ukb_selected_phenotypes.tab*: contains extracted phenotypes in tab-delimited file (similar to original tab file "ukbxxxx.tab").
- *_ ukb_selected_phenotypes.info*: shows information about phenotypes availability in the ukbxxxx.tab file, number of measure for each phenotype, and column location on both original and extracted tab file. [Click here to see example](data/ukbxxxxx_ukb_phenotypes.info)
--------------
### Available UKBB phenotypes at dhl_ec (UMC Utrecht)
- The lates version of UKBB phenotypes file (ukbxxxx.tab) in the HPC is `ukb44641.tab`.
- You can find the `ukb44641.tab` in this path.
```
/hpc/dhl_ec/data/ukbiobank/phenotypic/ukb44641.tab
```
##
### Slides
These slides have information about UKBB phenotypes at dhl_ec. [Click here to view slides](https://docs.google.com/presentation/d/1puiKuASZytYSQGJS6kJ629CmGbuVUW8pcx1X5H1gJAI/edit?usp=sharing).
##
### Contact
If you have any suggestions for improvement, discover bugs, etc. please create an [issues](https://github.com/CirculatoryHealth/UKBioPick/issues). For all other questions, please refer to the last author:
Abdulrahman Alasiri | a.i.alasiri [at] umcutrecht.nl
##
### License and copyright
[MIT License](LICENSE)
Copyright (c) 2021-2031 Abdulrahman Alasiri