ukb_rap_workflows

This repository contains documentation on how to run analyses on UKB_RAP

1. General overview: UKB_RAP_overview.md
2. How to: extract phenotypes data using dx: common_tasks/export_phenotypes.md
3. How to: web scrape UKB Showcase
   • Example script to scrape UKB Showcase to get the field-ids: codes/ukb_showcase_webscrape/ukb_showcase_webscrape.py
   • Note that the variables in this script are currently hard-coded. One needs to update some of the values to run for a field of interest
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