<p>Hi,</p>

<p>In various CNV analysis papers there is mention of excluding areas of the Genome from analysis</p>

<p>e.g. if the CNV spanned a centromere, if the CNVs overlapped at least 50% with regions previously defined as being prone to false positives due to somatic mutations, etc</p>

<p>Would anyone have a paper that details a list of which regions to exclude from CNV analysis, or a preprepared file for PLINK?</p>

<p>Best regards</p>

<p>Bob</p>

<p>There are several tracks in UCSC that might be useful for selecting regions to exclude from CNV analysis.  For example if you wanted to exclude near centromeres and telomeres, regions of high or low GC, assembly gaps, regions with poor mappability, repeat regions, etc.  Here are some examples of such tracks with links to their descriptions</p>

<ul>
<li><a href="http://genome.ucsc.edu/cgi-bin/hgTrackUi?&amp;c=chr17&amp;g=cytoBand">Chromosome Band</a></li>
<li><a href="http://genome.ucsc.edu/cgi-bin/hgTrackUi?&amp;c=chr17&amp;g=gap">Gap Locations</a></li>
<li><a href="http://genome.ucsc.edu/cgi-bin/hgTrackUi?&amp;c=chr17&amp;g=gc5Base">GC Percent</a></li>
<li><a href="http://genome.ucsc.edu/cgi-bin/hgTrackUi?&amp;c=chr17&amp;g=grcIncidentDb">GRC Incident</a></li>
<li><a href="http://genome.ucsc.edu/cgi-bin/hgTrackUi?&amp;c=chr17&amp;g=hiSeqDepth">HiSeq Depth</a> </li>
<li><a href="http://genome.ucsc.edu/cgi-bin/hgTrackUi?&amp;c=chr17&amp;g=wgEncodeMapability">Mappability</a></li>
<li><a href="http://genome.ucsc.edu/cgi-bin/hgTrackUi?&amp;c=chr17&amp;g=rmsk">Repeat Masker</a></li>
</ul>
