plink --file <name-without-map-or-ped-ending> --linear \
--pheno <name(.pheno)> --pheno-name <column> --covar \
--covar-name <names-of-covariants,separated,by,commas> \
--out <output-file-name-root> \
--noweb \ # don't check for update of PLINK
[--qq-plot] \ # gives expected distribution of p-values
[--adjust] \ # has some different ways of calculating p-val
[--hide-covar] # we don't need all this
plink --file <file-name> --freq --noweb
Really low-frequency results often produce false positives.