docs: def selectSNPsAccordingToLD(options):
      """Compute LD using Plink.
  
      :param options: the options.
  
      :type options: argparse.Namespace
  
      :returns: the name of the output file (from Plink).
  
      """
      # The plink command
      outPrefix = options.out + ".pruning_" + options.indep_pairwise[2]
      plinkCommand = [
          "plink",
          "--noweb",
          "--bfile", options.bfile,
          "--maf", options.maf,
          "--indep-pairwise",
      ] + options.indep_pairwise + ["--out", outPrefix]
  
      runCommand(plinkCommand)
  
      # Finding the autosomal markers
      autosomes = {str(i) for i in range(1, 23)}
      autosomal_snps = set()
      with open(options.bfile + ".bim", "r") as i_file:
          for line in i_file:
              chrom, snp = line.rstrip("\r\n").split("\t")[:2]
              if chrom in autosomes:
                  autosomal_snps.add(snp)
  
      # Reading the pruned markers
      pruned_snps = None
      with open(outPrefix + ".prune.in", "r") as i_file:
          pruned_snps = set(i_file.read().splitlines())
  
      # Writing the pruned markers located on an autosome
      with open(outPrefix + ".prune.in.autosomal", "w") as o_file:
          for snp in autosomal_snps & pruned_snps:
              print >>o_file, snp
  
      return outPrefix + ".prune.in.autosomal"