values of read positions having variations compared to reference (default: no)
</p>
</dd>
<dt class="hdlist1">
<strong>-descs</strong> [<em>yes|no</em>]
</dt>
<dd>
<p>
store read name for each read (default: no)
</p>
</dd>
<dt class="hdlist1">
<strong>-ureads</strong> [<em>yes|no</em>]
</dt>
<dd>
<p>
store unmapped reads in a separated fastq file (base name will be the value given in name and suffix will be " _unmapped.fastq" (default: no)
</p>
</dd>
<dt class="hdlist1">
<strong>-ref</st