Problem with logistic regression in Plink

Question

[C-man]

Hi

I have extracted snps from imputed bfile (plink) and I would like to run logistic with several diseases as a outcome.

Actually, raw file was an output for extract option. I changed it to bim, fam, bed and also tried map/ped

But, Odd ratios and p-value don't make any sense.

Here's my code for logistic. I have been trying several way

--bfile data --logistic --ci 0.95 --adjust --covar cova.txt --hide-covar --pheno outcomes.txt --missing-phenotype -999 --all-pheno --out

However, this code below did work well and I got p-value, but still I didn't know what does it mean because I do not know where is an outcome (disease)

--bfile data --logistic --ci 0.95 --adjust --covar cova.txt --hide-covar --out

Any thoughts on this?

Thanks