This section walks through the complete workflow for running Manc-COJO on UKB-RAP.

Step 1: Prepare inputs

  • Create a folder named WORK_FOLDER for the COJO analysis.
  • Download our software manc_cojo into WORK_FOLDER.
  • Prepare your GWAS summary statistics file at /SUMSTAT_FOLDER/Your_sumstat_file.
  • Generate your PLINK binary files to be used as LD references, with paths like /BFILE_FOLDER/Plink_bfile_chr${chr} (one per chromosome).

Step 2: Run Manc-COJO on UKB-RAP

Modify the paths and filenames as needed, then run the following command using DNAnexus Platform dx tools. Installation instructions and usage guidelines are available in the official DNAnexus documentation.

for chr in {1..22}; do

run_Manc_COJO="
cp manc_cojo \$HOME/manc_cojo && chmod +x \$HOME/manc_cojo

\$HOME/manc_cojo \\
--bfile \"/mnt/project/BFILE_FOLDER/Plink_bfile_chr${chr}\" \\
--cojo-file \"Your_sumstat_file\" \\
--out output_name \\
--cojo-slct \\
--thread-num 5
"
 
dx run swiss-army-knife \
-iin="Your_Project_ID:/WORK_FOLDER/manc_cojo" \
-iin="Your_Project_ID:/SUMSTAT_FOLDER/Your_sumstat_file" \
-icmd="${run_Manc_COJO}" \
--priority high \
--cost-limit 10 \
--ignore-reuse \
--instance-type mem3_ssd1_v2_x8 \
--destination="Your_Project_ID:/WORK_FOLDER" \
--tag Manc-COJO \
--tag chr${chr} \
-y \
--brief

done

Note that we set --thread-num 5 to speed up computation; this value can be adjusted depending on the compute resources available on UKB-RAP.