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@SimonYu668 Hi！I have met the same issue, Have you fixed that? Does it mean the MTAG can only be applied to the SNV other than indel ?

> > However, if you really want to retain those multi-allelic variants, there is a way to do so. You can try modifying your local version of the MTAG code...

Yeah; Thanks for your reply, But I wonder that does it mean MATG can only be applied to the SNV other than indel?

Thank you for your response! I've noticed that including only SNVs works well. Moreover, when utilizing the European reference panel, it effectively manages indels, unlike with other reference panels where...

Dear professor， It seems that MTAG produces higher effect, How to explain it？Is it normal? Attached is the log file. Hope for your response. Thanks! Change is great and seems...

Thanks for your reply. More specifically, I compared the raw results of SNP from GWAS summary data and the results of MTAG. I found the effect size of some snps...

Thank you. But I have normlized the phenotype during GWAS analysis. So whether the beta in the MTAG analysis can be used for report?

Thank you again for your patience in answering my questions.

However，I noticed that some snps effect has also changed. Is it also Normal？Is there any soultions to these snp like heterogeneity test in meta analysis? RAW phenotype1 GWAS summary：beta=-0.008；SE=0.02；P=0.622 RAW...

yes