Pipeline Overview

The stages of the pipeline are separated into numbered modules. While many of the initially modules are sequential and require the prior modules to have been completed. From module 03 onwards, they don't necessarily need to be completed in numerical order. This flowchart represents the dependencies between the individuals scripts and shows how the scripts depend upon each other.

Modules ready to be run

Below is a list of modules that are ready to be run. We encourage you to run as many of these as possible. Specific instructions for how to run each of these can be found on the individual module pages. There is a navigation menu to these on the right hand side of the wiki.

0-03 – system set-up and data checks

04 - mQTLs

07 – variance QTLs

08 – inversion mQTLs

09 – PRS EWAS

10 – epigenetic age GWAS

11- smoking GWAS

14 – nc886 GWAS