code: def mpileup(args):
      
      p = OptionParser(mpileup.__doc__)
      opts, args = p.parse_args(args)
  
      if len(args) < 2:
          sys.exit(not p.print_help())
  
      prefix, ref = args[0:2]
      bams = args[2:]
      cmd = "samtools mpileup -P ILLUMINA -E -ugD -r {0}"
      cmd += " -f {0} {1}".format(ref, " ".join(bams))
      fmd = "bcftools view -cvg -"
      seqids = list(Fasta(ref).iterkeys_ordered())
      for s in seqids:
          outfile = prefix + ".{0}.vcf".format(s)
          print(cmd.format(s), "|", fmd, ">", outfile)
docs: %prog mpileup prefix ref.fa *.bam
  
      Call SNPs using samtools mpileup.