This repository contains documentation on how to run analyses on UKB_RAP
- General overview:
UKB_RAP_overview.md - How to: extract phenotypes data using dx:
common_tasks/export_phenotypes.md - 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
- Example script to scrape UKB Showcase to get the field-ids:
- 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