SNPTEST v2.5.4 for GWAS analysis

Question

[Cindy]

Hi all,

I am using SNPTEST V2.5.4 to run GWAS analysis. the method newml gives two P values: wald test P and likelihood P, which are different. Which one I should use?

I used Plink to run logistic regression to compare the P values with SNPTEST, the wald-P in PLINK is close to the likelihood P in SNPTEST.

Please help. Appreciate in advance.

Answer 1

[KS]

Hi,

I am facing same problem, were you able to figure it out. Also did you run this method newml on chromosome X data?

Thanks