Regarding the use of output

[HongyanR]

Hi, a quick question, can I carry out a meta-analysis using mtag outputs, as I understand several files will be generated using MTAG. My goal is to generate one file of the common factor for the traits I use. Thanks!

[paturley]

Hello! If you use the meta-analysis option, the files should be identical, so any of them should do. We talked about changing the code so that it only produces one set of summary statistics, but I don't know if we have gotten around to implementing that yet. Thoughts, @huilisabrina ?

[huilisabrina]

Hi @HongyanR ,

That's right @paturley so you can turn on this meta-analysis mode, by specifying two flags simulaneously - --equal_h2 and --perfect_gencov. With this mode, MTAG produces a single set of sumstats, where the betas are unstandardized using 2p(1-p) where p is the average allele frequencies across traits.

Best, Hui