paturley

We recently noticed something that looked like a software bug in the beta-SE option, so we flipped it off until we can look into it. For now, you'll need to...

You can calculate Z using Z = beta/SE and I bet the N is reported in the associated paper if you looked it up. Best, Patrick On Tue, Mar 22,...

Hello! I believe that the the log file has a table that includes a columns corresponding to "GWAS-equivalent N". Are you able to find that table in the log file?

Apologies for the delayed response here. My hands have been quite full. Do you mind sending me a copy of the log file? That may help me know how to...

Hello both of you. Sorry for the delayed response. This has been a puzzle to me and I've had to take some time to think about it. The GWAS equivalent...

Hello! I believe that the the log file has a table that includes a columns corresponding to "effective N". Are you able to find that table in the log file?...

Hi Anuj, I'd recommend trying to use the n_appox flag. Especially if your summary statistics have approximately the same sample size across all SNPs within each trait. On Thu, Dec...

I'm sure it is. With 5 phenotypes, it's searching along 2^5 axes of variation and it's likely checking 100 points for each axis. So it is evaluating the FDR at...

Hi Julia, There are many filters that MTAG imposes beyond allelic consistency. It's hard to diagnose the problem without seeing the data. Can you share the row of the summary...

MTAG includes a number of filters by default, including any filters imposed by ldsc. (Which includes indels, I believe.) Have you looked over the documentation to confirm that there are...