Colocalization analysis pipeline

1. Lift coordinates

Execute ./lift.sh to lift GWAS variant coordinates from GRCh36 to GRCh38.

2. Prepare input files

Run prep_input_coloc.R to create input files formatted for eQTL Catalogue queries and coloc.

3. Query eQTL catalogue and perform colocalization

Run the script run_coloc.R to obtain data from eQTL catalogue and perform colocalization.

This step was performed in an interactive job with 8 CPUs and 64GB of RAM.