I have used two different methods to do a height GWAS, and would like to know which method has more statistical power. I've searched over the internet and found that most software products are either

- not available anymore (obsolete links) or
- only available online (implying manual input for millions of snps) or
- irrelevant (e.g. to help calculate sample size for a to-be-planned GWAS).

The only package seems to be appropriate is GWAS power at https://github.com/kaustubhad/gwas-power, but I have a question regarding which p-value to use (https://github.com/kaustubhad/gwas-power/issues/3) and not sure when the question will be answered.

The above being said, I am wondering how people are calculating GWAS power these days.

A related question is what metrics to use to tell which GWAS method is better than the other besides power. Suggestions would be appreciated.

Thanks much in advance!

Hi Kevin,

Thanks for the reply. I had checked out CaTS before posting above. However, I am not sure if CaTS does what I want to do.

Suppose I have two linear regression models for GWAS:

After the GWAS is done, that is to say, all the betas, SEs, p-values are generated for each of the models, I want to see which model gives more power. Can CaTS calculate the actual power of the models so that we can compare which model is more powerful? If I understand correctly, CaTS only estimates (not calculates?) the power of a GWAS design before the GWAS is conducted.

Thanks.