ine/A375.bam 127
AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT Hg38 TOP ./reference/hg38.fa
./reference/simpleRepeat.bed.gz</p>
</div>
<div id="file-4-reference-genome-human-hg38-or-hg19-or-mouse-mm10" class="section level1">
<h1>File 4: Reference genome: Human (hg38 or hg19) or Mouse (mm10)</h1>
<p>(optional, but mandatory with cram files)</p>
</div>
<div id="file-5-simple-repeat-region-bed-file" class="section level1">
<h1>File 5: simple repeat region bed file</h1>
<p>(optional, but mandatory to detect simple repeat 