Hui Li

Hi @julyankb , Could you try lowering the precision of the pvalues when you pre-process/QC the input data? The error happened when MTAG calls a LDSC module to munge the...

Hi @aydzhouyuan , Did Patrick's answer solve your question? Feel free to close this issue if you don't have further questions. Thanks, Hui

Hi, Thanks for raising this question. Which link did you mean? There are two steps that you might be talking about, one is the Anaconda installation, the other is to...

Hi @WDHill , That link may be outdated (I didn't write the original README file so it slipped my attention). I just swapped it with another one. Hopefully this new...

Hi @umcyh , The error comes from one of the data validity checks built in the LDSC package, which MTAG uses to estimate the Sigma. To your questions: (1) You’re...

Hi @GeneticResources , One possibility is that the N used in the case-control trait is not the "effective N". MTAG assumes SE=1/sqrt(N_eff*2*p*(1-p)), where p is the minor allele frequency. Can...

Hi @jianvhuang , One possibility is that the variants in your input sumstats are not formatted correctly. From the log it seems that you're using the default LD reference panel...

@paturley Yes I'll add this in the next round of revision, which will happen soon!

Hi @jineexia , I've added the check of chi2 in the updated version of MTAG. Please re-pull the master branch for future runs. If your question has been resolved, feel...

Hi @Julia-Ramirez , MTAG adopts some of the basic filters used in the munging step of [ldsc](https://github.com/bulik/ldsc/wiki/Heritability-and-Genetic-Correlation#reformatting-summary-statistics), one of which is dropping multiallelic variants. For the specific SNP you mentioned,...