Hi,

I was conducting the conditional analysis for GWAS summary statistic based on several SNPs I selected and --cojo-cond, but got the error

Error: there is a collinearity problem of the given list of SNPs. 
You can try the option --cojo-slct to remove one of each pair of highly correlated SNPs. 
An error occurs, please check the options or data

I then added the --cojo-slct but found that the --cojo-slct selected the independent SNPs from the GWAS summary stats automatically and performed the conditional analysis based on those SNPs. It ignored the SNPs I provided.

So I think I can't use both --cojo-slct and --cojo-cond at the same time.

Does anyone know how to solve this problem?

Thank you.