case control association analysis with covariates in plink?

Question

[Sheila]

Hi!

I would like to complete a case/control analysis with two covariates (sex and age) in plink. Here is my model

Y = B0 + B1X1 + B2X2 + B3X3

where... Y = Disease Status (0 or 1), X1 = given SNP, X2 = Sex, X3 = Age

I have a few questions:

This was my command:

plink --bfile myfile --assoc --covar --covarList.cov --out results

I realized i couldn't include covariates in a case control analysis in plink. That being said, would the --linear command provide me what I need (See command below)???

plink --bfile myfile --linear --covar --covarList.cov --out results

Would I need to create a pheno file if I use the --linear command or would the command above give me the results.

I basically am asking what is the correct command to achieve the results of my given model above.

Thank you!

Answer 1

[chrchang523]

--logistic is the command you're looking for.