paturley

Hi Chen, Many SNPs appear to be dropped during the MTAG QC process. If you just consider the set of overlapping SNPs between the GWAS and MTAG files, does it...

Are you you using the Z-N option or the beta-SE option? We've noticed a few things that look like bugs in the beta-SE option recently, so it may be that...

1. I recommend that you use the effective N formula from https://www.nature.com/articles/nprot.2014.071. 2. Running MTAG by chromosome is fine. The only consideration is that the Sigma and Omega matrix will...

Hi Kijoung, Yes. The reason the results may differ is that Omega and Sigma are forced to be the same if you run it all together and they are allowed...

Hey. Not totally sure what is driving the discrepancy, but there are a number of possibilities. MTAG's SNP filters are a little different than LDSC's filters, so it could be...

Hello, I agree that an important assumption of MTAG is that the LD score used is sufficiently similar to the true population LD score for the populations corresponding to each...

Hi, I don't know that I totally understand your concern, but it sounds like a general critique of LD score regression. If you have concerns that these issues you are...

My guess is that a CM map is not necessary. I think we likely inherited that code from LD score regression since there is no clear reason to me why...

Hello Kai, It looks like there may be a problem with your Phenotype 13 or 14. Can you verify that there are no NaN in any of the columns in...

Sorry for the delayed response here. Had a grant due late last week. Your traits 2 and 3 in that log have a really high LD score intercept. Any idea...