Logistic regression?

[Jolleboll]

Hello, apologies if this is a really dumb question.

I have been tasked to perform a "GWAS analysis" on some genotype data. I usually do this in R with a logistic regression model, but I thought I'd try vcf2gwas instead. However, I don't see logistic regression among the model options. Or is it equivalent to -lmm --multi? But there is no option to specify what phenotype variable to be the "outcome" variable, if you know what I mean. Is it the first one specified?

Please excuse my statistics ignorance :)

Joel

EDIT: I think I'm beginning to confuse or de-confuse myself. The adding of covariates is probably what I was trying to do... and the -p option variables are the ones that will be "predicted", ja?