genomicsengland / gel_cohort_overlap

GEL Overlapping Cohorts

The purpose of this repo is to :

• Gather demographic data for participants in a given GEL cohort
• Maintain the utilities to format, filter and generate hashes based on a defined algorithm

Demographic Data

• Demographic data is pulled using the query defined in the /sql folder. This query is run against the Patient Master Index (PMI)

File Name	Description
pmi_demographics.sql	Gathers nhs_number and date_of_birth for all participants in the 100k study that are within the PMI

DotEnv

• A .env file (part of gitignore, so is local to the running machine) is required in the root of the repo. The structure of this file is available in the dotenv.tmpl file

Usage

• A /data folder should be created in the root of the repo to store output data
• main.py - Collates all utilities and runs in the required order