code: def passthrough(args):
      
      p = OptionParser(passthrough.__doc__)
      opts, args = p.parse_args(args)
  
      if len(args) != 2:
          sys.exit(not p.print_help())
  
      vcffile, newvcffile = args
      fp = open(vcffile)
      fw = open(newvcffile, "w")
      gg = ["0/0", "0/1", "1/1"]
      for row in fp:
          if row[0] == "#":
              print(row.strip(), file=fw)
              continue
  
          v = VcfLine(row)
          v.filter = "PASS"
          v.format = "GT:GP"
          probs = [0] * 3
          probs[gg.index(v.genotype)] = 1
          v.genotype = v.genotype.replace("/", "|") + \
                  ":{0}".format(",".join("{0:.3f}".format(x) for x in probs))
          print(v, file=fw)
      fw.close()
docs: %prog passthrough chrY.vcf chrY.new.vcf
  
      Pass through Y and MT vcf.