Question: Output of METAL meta-analysis: which allele does the beta refer to?
gravatar for smnlalli
5.6 years ago by
smnlalli0 wrote:


I have run a meta-analysis using METAL, and I have an output file (ending in ".tbl") including an "Effect" column and an "Allele1" and "Allele2". I would like to compare the effect column of this analysis to another dataset, but in order to do so I need to align the betas depending on which allele the effects refer to. I was wondering if I can assume that the effect is computed for the allele specified in the "Allele1" field.

The Wiki documentation for METAL talks about the first study included in the meta-analysis being used as the reference for the alleles, so if I am understanding this correctly the "Effect" is expressed in reference to "Allele1". If this is not the case, how can I find the allele that is used as the effect allele? 

Thank you very much for all your help,


meta-analysis metal • 3.8k views
ADD COMMENTlink modified 6 weeks ago by Olliepain0 • written 5.6 years ago by smnlalli0

What's the answer? I think I met the same question.

ADD REPLYlink written 6 weeks ago by hexiaoxi.2312320
gravatar for Olliepain
6 weeks ago by
Olliepain0 wrote:

METAL creates a file when running the analysis which describes the output. It states that the Effect column corresponds to the "overall estimated effect size for allele1".

ADD COMMENTlink written 6 weeks ago by Olliepain0
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