s="kw">;</span> <span class="kw">done</span></span>
<span id="cb4-31"><a href="#cb4-31"></a></span>
<span id="cb4-32"><a href="#cb4-32"></a></span>
<span id="cb4-33"><a href="#cb4-33"></a><span class="co"># Make a text-file list of the BAMs</span></span>
<span id="cb4-34"><a href="#cb4-34"></a><span class="ex">/map/--%</span> ls -1 *sorted.bam <span class="op">&gt;</span> bamlist.txt</span>
<span id="cb4-35"><a href="#cb4-35"></a></span>
<span id="cb4-36"><a href="#cb4-36"></a></span>
<span id="cb4-37"><a h