Coloc pipeline for nominal QTLtools output:

Note: This pipeline assumes that the QTLtools analysis was performed using whole chromosomes as regions. You need a QTLtool output file for each chromosome.

1- Run coloc_file_prep.sh
	-This shell script runs coloc_file_prep.R to prep the QTLtools output for coloc analysis

2- Run coloc.sh
	-This shell script runs coloc.R to run coloc analysis using input from previous step
	-This script also takes as input the gwas cad data info

3- Run biomart_annotate_coloc.sh
	-This shell script runs biomart_annotate_coloc.R to annotate the summary dataframe output from coloc analysis
	-The annotation includes gene name, chromosome number, and chromosome start

4- Run coloc_concat_results.R (Optional)
	-This R script concatenates the annotated coloc results for all 22 chromosomes