Use case for COJO:
User wants to run the COJO for a specific locus, having only locus-wide (not genome-wide) summary stats
How it works now:gcta --bfile <bfile> --cojo-p <p treshhold> --extract <snp.list.in.locus> --cojo-file <locus_wide_summary_stats> --cojo-slct --out <output_file>
Problem:
gcta COJO will calculate trait variance based on locus-wide summary stats. But according to the instructions, user should not do this. Although, instructions propose to combine input of full GWAS summary stats with --extract option, this does not help, when user does not have full GWAS summary stats.
2) Please always input the summary statistics of all SNPs even if your analysis only focuses on a subset of SNPs because the program needs the summary data of all SNPs to calculate the phenotypic variance. You can use one of the --extract options (Data management) to limit the COJO analysis in a certain genomic region. https://yanglab.westlake.edu.cn/software/gcta/#COJO
Request
Can you please add kinda --var <trait variance>, so user can specify the trait variance with no need to estimate it from input summary stats?
Use case for COJO: User wants to run the COJO for a specific locus, having only locus-wide (not genome-wide) summary stats
How it works now:
gcta --bfile <bfile> --cojo-p <p treshhold> --extract <snp.list.in.locus> --cojo-file <locus_wide_summary_stats> --cojo-slct --out <output_file>Problem: gcta COJO will calculate trait variance based on locus-wide summary stats. But according to the instructions, user should not do this. Although, instructions propose to combine input of full GWAS summary stats with
--extractoption, this does not help, when user does not have full GWAS summary stats.Request
Can you please add kinda
--var <trait variance>, so user can specify the trait variance with no need to estimate it from input summary stats?Sodbo Sharapov sodbo.sharapov@fht.org