ukb_rap_workflows

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.

1. General overview and resources for getting started on the RAP system: UKB_RAP_overview.md
2. How to: extract phenotype data using dx: common_tasks/export_phenotypes.md
3. How to: web scrape UKB Showcase: codes/ukb_showcase_webscrape/ukb_showcase_webscrape.py
4. How to: create the file to use as input for dx extract_dataset: codes/export_phenotypes/subset_all_fields.py
5. How to: run PHESANT: run_phesant/run_phesant_readme.md
6. How to: subset pVCF files for a region/gene of interest: wes_analyses/wes_analyses_readme.md
7. How to: Run GWAS in plink using (local) CTG pipeline settings: gwas_analyses/gwas_readme.md
8. How to work with data and files interactively: interactive_workspaces.md
9. How to create polygenic scores in UKB using PRScs: prscs-calculation.md
10. How to create an applet: [applet_example_readme.md] (https://github.com/vu-ctg/ukb_rap_workflows/blob/master/codes/applet_example/applet_example_readme.md)
11. How to run MAGMA gene-based analyses and create gene burden scores.

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.