This repository contains documentation for VU-CTG lab members on how to run analyses on the UK Biobank Research Analysis Platform (UKB-RAP). The scripts contained here are meant to follow pipelines developed within the VU-CTG lab and may not be suitable for other applications. For more information about the platform, please consult the UKB-RAP website, its documentation site, or the UKB online community help pages.
Before working with the RAP, make sure you have completed your Researcher Training Courses - mandatory for accessing the system. It is also a good idea to review the series of webinar tutorials to get familiar with the platform.
- General overview and resources for getting started on the RAP system:
UKB_RAP_overview.md - How to: extract phenotype data using dx:
common_tasks/export_phenotypes.md - How to: web scrape UKB Showcase:
codes/ukb_showcase_webscrape/ukb_showcase_webscrape.py - How to: create the file to use as input for
dx extract_dataset:codes/export_phenotypes/subset_all_fields.py - How to: run PHESANT:
run_phesant/run_phesant_readme.md - How to: subset pVCF files for a region/gene of interest:
wes_analyses/wes_analyses_readme.md - How to: Run GWAS in plink using (local) CTG pipeline settings:
gwas_analyses/gwas_readme.md - How to work with data and files interactively:
interactive_workspaces.md
Coming soon: how to run MAGMA gene-based analyses and polygenic score analyses.
Developing a new analysis not already documented here? Have a helpful RAP tip to share? Feel free to add to this repository or contact @jesavage to be added as a contributor.