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<p>Hi Margaret,</p>
<p><br>
</p>
<p>Sorry for the delay.</p>
<p>The stats written out in stats_html are collected internally
simultaneously with the VEP annotation and therefore are not
generated based on the VCF columns of the output file.<br>
</p>
<p><br>
</p>
<p> Depending on what VEP run options were selected, the counts
could be reproduced based on the output file. For example the
number of overlapped genes corresponds to the unique count of ENSG
identifiers in the 'Gene' output column. The number of overlapped
transcripts and regulatory features could be computed based on the
'Feature' and 'Feature_type' columns.<br>
</p>
<p><br>
</p>
<p><br>
</p>
<p>Kind regards,</p>
<p>Irina<br>
</p>
<p><br>
</p>
<div class="moz-cite-prefix">On 12/09/2019 19:27, Linan, Margaret
wrote:<br>
</div>
<blockquote type="cite"
cite="mid:6bcf55004f5247a4874c04ff54cfa93b@mssm.edu">
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<p>Hi -</p>
<p><br>
</p>
<p>Does anyone know how the VEP command line program's
stats_html utility calculates the following (i.e., what VCF
columns and operations it uses)?</p>
<blockquote>
<p>- VCF file pre-processing</p>
<p>- Number of overlapped genes</p>
<p>- Number of overlapped transcripts</p>
<p>- Number of overlapped regulatory features<br>
</p>
</blockquote>
<p><br>
</p>
Thank you,
<p>Margaret<br>
</p>
</div>
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