Jonathan Jala

After checking the code, it appears that the usage documentation is erroneous (or at least incomplete....the --use-beta-se option would also need to be specified for MTAG to use the beta...

Yes, if the panel is not specified, it uses the eur_w_ld_chr included in MTAG by default. You should be able to generate an LD score panel using the ldsc_mod code...

Looks like this is breaking on the LD score regression step. If you pass your summary statistics into LDSC to calculate genetic correlation, do you see this same error?

Interesting, ok. I don't believe we've seen the error before, and from trying to do a little online research it sounds like it's an error bubbling up from farther down...

Hello, Have you tried using the "--ld_ref_panel" flag? (running "mtag.py -h" will give you a breakdown of the different flags and options) That will allow you to pass in a...

The panel that comes with MTAG looks to be about 55MB. Is 120G how large the directory you're specifying is? What you're trying to use is over 2000 times the...

Ah ok. You could try removing the annotated columns for what you send into MTAG, since that will reduce the size of things by almost a factor of 200. See...

It looks like the pull request that was implemented about 10 months ago to add a median z cutoff to mtag.py made the assumption that munge would be called from...

The force option has the description "Force MTAG estimation even though the mean chi2 is small.", so that won't really help there. If you're hitting a stop at that particular...

Just updated the tutorial to point to thessgac.com. It does require registering for an account, but once that is done, then just download the Okbay et. al. 2016 summary stats...