iv>
<div id="data-pre-processing-tools" class="section level2" number="7.8">
<h2><span class="header-section-number">7.8</span> Data pre-processing tools</h2>
<p>In most cases, all of these tools will be used sequentially to prepare the data for downstream mutational and copy number variation (CNV) analysis.<br />
- <a href="https://bedtools.readthedocs.io/en/latest/">Bedtools</a> including the bamtofastq function, which is the first step in converting data off the sequencer to a usable format for downstrea