mtag
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JonJala
Python command line tool for Multi-Trait Analysis of GWAS (MTAG)
Dear authors and users, I ran maxFDR on each of the sets of summary statistics separately to estimate their corresponding basline maxFDR as suggested by paturley (https://github.com/omeed-maghzian/mtag/issues/61#issuecomment-460291600). It worked for...
Hi, I am comparing two big GWAS from the same paper. They are both big meta-analysis with the same sample, but from two different traits. For both sets of SNPs...
Dear Omeed, When running MTAG on the GWAS results of two related traits (UKB data, phenotypic correlation 0.6), with sample overlap, I picked up some loci that were not significant...
Dear sir, I have improved my previous mtag input after reading all the issues, I used the effect sample size to be the N column, but I still can't get...
Thanks for your reply. When running the MTAG, I get an error message just like some others have, the mean chi2 statistic of triat 2 is less than 1.02, I...
Hi there, Recently, I combined 4 different traits using MTAG without any error or warning. However, I concern about the lambda inflation factor because the lambda is higher than expected....
Hi, There seems to be a mistake in the code for computing mtag factors reported in the log. I've always been puzzled by weird weights reported by MTAG and noticed...
Hi, I have git cloned the MTAG directory and created the conda environment. mtag.py works just fine but both ldsc.py and munge_sumstats.py do not work at all. python ldsc.py -h...
Hi, Thanks in advance! I encountered two problems: 1. WARNING: 159 SNPs had P outside of (0,1]. The P column may be mislabeled. - I do check my data in...
Hi all, My summary data lacked the maf column. When I tried to run mtag. I got the following error: Traceback (most recent call last): File "/ysm-gpfs/pi/zhao/mc2792/software/mtag/mtag.py", line 1567, in...
