Post by mocksu on Sept 5, 2021 3:03:37 GMT
I am trying to do two sample Mendelian Randomization. As the first step, I need to find independent signals (SNPs) that are associated with a protein level. I have a full summary stat file for the pQTL of the protein. I used ""gcta64 --bfile <my_ref_in_plink_bfile_format> --cojo-file <my_full_smmary_stats_file> --cojo-wind 20 --cojo-slct --extract <my_pval<5e-8_summary_stats_file> --out <my_output>".
The problem is that 6-10 independent signals are expected while I keep getting 1 independent signal, regardless the --cojo-wind size (10MB, 1MB, 200kb, 20kb, 10kb) and --cojo-collinear (0.9, 0.99 tried) used.
Any comments/suggestions would be highly appreciated.
Thanks in advance!