ttempt to read from STDIN.</p></td>
    </tr>
    <tr>
      <th>out</th>
      <td><p>Output file name. The script can write to STDOUT by
specifying STDOUT as the output file name - this will force quiet mode.
Default = 'variant_effect_output.txt'</p></td>
    </tr>
    <tr>
      <th>fasta</th>
      <td><p>Specify a FASTA file or a directory containing FASTA files to use to look up reference sequence.
The first time you run the script with this parameter an index will be built
which can take a few minute