docs: def extractSNPs(snpsToExtract, options):
      """Extract markers using Plink.
  
      :param snpsToExtract: the name of the file containing markers to extract.
      :param options: the options
  
      :type snpsToExtract: str
      :type options: argparse.Namespace
  
      :returns: the prefix of the output files.
  
      """
      outPrefix = options.out + ".pruned_data"
      plinkCommand = ["plink", "--noweb", "--bfile", options.bfile, "--extract",
                      snpsToExtract, "--make-bed", "--out", outPrefix]
      runCommand(plinkCommand)
      return outPrefix