This repository contains code and data for performing colocalization analysis in Jeong and Bulyk (2023). The repository for code to generate figures in the manuscript is here.
Raehoon Jeong (rjeong@g.harvard.edu), Martha Bulyk Lab (mlbulyk@genetics.med.harvard.edu).
- GWAS summary statistics and PU.1 bQTL data for tested loci are in
Coloc/data. - Coloc results are in
Coloc/results. - Code to reproduce the results are in
Coloc/scripts. The code took ~1.5 hr to run on a computing cluster. - Need to install Coloc to run the code.
cd ${THIS_DIR}/Coloc/scripts
# The code expects R/3.6.3
# It currently loads a module, but feel free to comment it out
bash job_run_coloc.sh
- GWAS summary statistics and PU.1 phenotype and genotype data for tested loci are in
JLIM/data. - JLIM results are in
JLIM/results. - Code to reproduce the results are in
JLIM/scripts. The code takes ~ 2hr for each locus on a computing cluster, and there are 1623 loci. So the repo also includes an example script for parallel job submission. - Need to install JLIM to run the code. At this time, JLIM v2.5 is released, and here, we uploaded JLIM v2.0 scripts that can run with JLIM v2.5.
cd ${THIS_DIR}/JLIM/scripts
# The code expects R/3.6.3 and python 2.7
# It currently loads a module, but feel free to comment it out
bash job_run_jlim_all_loci.sh # This might take long
# bash job_run_jlim_parallel.sh # This submits jlim analysis jobs by blood cell trait and chromosome