Mahan

Trouble getting the model performance in LDPred2

1

Hi Florian, I'm using the following codes to obtain the final model summary and I have some troubles as my target variable is binary. Can you suggest how I can...

How to get CHR & POS info on Hg38 using rs Id information?

2

I have a list of SNP rs ids (>1M) for which I would like to find the CHR & POS information. Can you please suggest a suitable tutorial or Jupyter...

How does MTAG handle duplicate rs ids and variants that are not SNPs?

1

When I run MTAG I see logs about duplicate rs numbers and variants that are not SNPs being filtered. I would like to know how does MTAG handle these?

Could not open /usr/local/bin/ld_ref_panel/eur_w_ld_chr/1.l2.ldscore[./gz/bz2]

8

I'm trying to run MTAG with default options and I'm getting following error: Could not open /usr/local/bin/ld_ref_panel/eur_w_ld_chr/1.l2.ldscore[./gz/bz2] How can I address this issue? TIA

Due to bugs in the beta-se code, this option has been temporarily removed from the MTAG software

8

How can I address the following error? File "mtag.py", line 1546, in raise RuntimeError("Due to bugs in the beta-se code, this option has been temporarily removed from the MTAG software....

Summary Stats without EAF & Sample size

9

I have 3 summary stats out of which two of them do not have EAF & sample size columns. I would like to know how I proceed further to use...

Do you have tutorial to work with high dimensional data like SNP data?

How to use OVERLAP ON option?

1

I'm trying to perform the meta-analysis of two GWAS studies and I would like to correct for the overlapped samples. Could you please share an example code with OVERLAP ON?

Unable to run MTAG with --use_beta_se flag

4

Hello, I'm trying to run MTAG with beta and SE, using the instructions from here: **Note: If both the effect sizes and the standard errors are present in the input...