code: def freq(args):
      
      p = OptionParser(freq.__doc__)
      p.add_option("--mindepth", default=3, type="int",
                   help="Minimum depth [default: %default]")
      p.add_option("--minqual", default=20, type="int",
                   help="Minimum quality [default: %default]")
      p.set_outfile()
      opts, args = p.parse_args(args)
  
      if len(args) != 2:
          sys.exit(not p.print_help())
  
      fastafile, bamfile = args
      cmd = "freebayes -f {0} --pooled-continuous {1}".format(fastafile, bamfile)
      cmd += " -F 0 -C {0}".format(opts.mindepth)
      cmd += ' | vcffilter -f "QUAL > {0}"'.format(opts.minqual)
      cmd += " | vcfkeepinfo - AO RO TYPE"
      sh(cmd, outfile=opts.outfile)
docs: %prog freq fastafile bamfile
  
      Call SNP frequencies and generate GFF file.