".glm.firth.hybrid" output file in plink2 does not give correct CASE_ALLELE_CT values

Question

[L_to_the_m]

Hi, I have been doing a GWAS with PLINK2 and got an output file with the extension: .glm.logistic.hybrid command. Everything worked fine until I realized that the output values are not really conform with my phenotype values.

For example: For each sample I got phenotypes in binary format (0's and 1's). Here I have 347 samples with 0's (controls) and 194 with 1's (cases).

The output from PLINK2 gives me within the column CTRL_ALLELE_CT (specified by plink2 index as: Control allele observation count): 598 And in the column: CASE_ALLELE_CT (specified by plink2 index as: Case allele observation count): 304

Obviously these are not the correct case and control counts. How can this be? What exactly is PLINK2 measuring here?

Answer 1

[chrchang523]

Answered at https://groups.google.com/g/plink2-users/c/QHnD0FTKuks .