plink.md

Linear Regression With PLINK

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

Get allele Frequency

plink --file <file-name> --freq --noweb

Really low-frequency results often produce false positives.