Skip to content

new cohorts

Jump to bottom
epzjlm edited this page Sep 4, 2025 · 4 revisions

You can still join DEEP if you have a cohort with more than 100 individuals with genetic and DNA methylation data. We released the pipeline in September 2025. Please contact Josine Min or Hannah Elliott for more details.

Data preparation prior to pipeline

Pipeline set up

QC stage 01 (ready)

0. Set up folders
1a. Check data
1b. Process genetic data
1c. Check methylation and phenotypes
1d. mQTL control GWAS
1e. GWAS of genetic PCs
1f. Cross-cohort normalisation of methylation data
1g. Compute haplotype components
1 upload. Upload to Bristol SFTP

The pipeline modules (under development)

2a. Relatedness assessment/removal
2b. Regular and variance EWAS
3a. Run meQTL analysis
3b. Run variance meQTL analysis

Instructions for developers

Clone this wiki locally