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.