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<p>Hi Margaret,</p>
<p><br>
</p>
<p>To get an accurate count for overlapping transcripts you would
need to count the unique identifiers in the 'Feature' column for
the records that have '<i>Transcript</i>' in the 'Feature_type'
column.</p>
<p>A similar count would be needed for regulatory features: counting
the unique identifiers in the 'Feature' column for the records
that have '<i>RegulatoryFeature</i>' in the 'Feature_type' column.</p>
<p>Counting the occurrences of "<i>Transcript</i>" in the 'Feature'
column will result in double counting any transcript that is
affected by more than one of the input variants.</p>
<p><br>
</p>
<p>'sense_overlapping' indicates that the variant is on a long
non-coding transcript that contains a protein coding gene within
its intronic sequence on the same strand, with no overlap of
exonic sequence.<span style="color: rgb(51, 51, 51); font-family:
"Luxi Sans", Helvetica, Arial, Geneva, sans-serif;
font-size: 12.8px; font-style: normal; font-variant-ligatures:
normal; font-variant-caps: normal; font-weight: 400;
letter-spacing: normal; orphans: 2; text-align: left;
text-indent: 0px; text-transform: none; white-space: normal;
widows: 2; word-spacing: 0px; -webkit-text-stroke-width: 0px;
background-color: rgb(255, 255, 255); text-decoration-style:
initial; text-decoration-color: initial; display: inline
!important; float: none;"><br>
</span></p>
<p><span style="color: rgb(51, 51, 51); font-family: "Luxi
Sans", Helvetica, Arial, Geneva, sans-serif; font-size:
12.8px; font-style: normal; font-variant-ligatures: normal;
font-variant-caps: normal; font-weight: 400; letter-spacing:
normal; orphans: 2; text-align: left; text-indent: 0px;
text-transform: none; white-space: normal; widows: 2;
word-spacing: 0px; -webkit-text-stroke-width: 0px;
background-color: rgb(255, 255, 255); text-decoration-style:
initial; text-decoration-color: initial; display: inline
!important; float: none;"><br>
</span></p>
<p><span style="color: rgb(51, 51, 51); font-family: "Luxi
Sans", Helvetica, Arial, Geneva, sans-serif; font-size:
12.8px; font-style: normal; font-variant-ligatures: normal;
font-variant-caps: normal; font-weight: 400; letter-spacing:
normal; orphans: 2; text-align: left; text-indent: 0px;
text-transform: none; white-space: normal; widows: 2;
word-spacing: 0px; -webkit-text-stroke-width: 0px;
background-color: rgb(255, 255, 255); text-decoration-style:
initial; text-decoration-color: initial; display: inline
!important; float: none;"></span><br>
Kind regards,</p>
<p>Irina<br>
</p>
<p><span style="color: rgb(51, 51, 51); font-family: "Luxi
Sans", Helvetica, Arial, Geneva, sans-serif; font-size:
12.8px; font-style: normal; font-variant-ligatures: normal;
font-variant-caps: normal; font-weight: 400; letter-spacing:
normal; orphans: 2; text-align: left; text-indent: 0px;
text-transform: none; white-space: normal; widows: 2;
word-spacing: 0px; -webkit-text-stroke-width: 0px;
background-color: rgb(255, 255, 255); text-decoration-style:
initial; text-decoration-color: initial; display: inline
!important; float: none;"><br>
</span></p>
<p><span style="color: rgb(51, 51, 51); font-family: "Luxi
Sans", Helvetica, Arial, Geneva, sans-serif; font-size:
12.8px; font-style: normal; font-variant-ligatures: normal;
font-variant-caps: normal; font-weight: 400; letter-spacing:
normal; orphans: 2; text-align: left; text-indent: 0px;
text-transform: none; white-space: normal; widows: 2;
word-spacing: 0px; -webkit-text-stroke-width: 0px;
background-color: rgb(255, 255, 255); text-decoration-style:
initial; text-decoration-color: initial; display: inline
!important; float: none;"><br>
</span></p>
<p><br>
</p>
<div class="moz-cite-prefix">On 16/09/2019 18:25, Linan, Margaret
wrote:<br>
</div>
<blockquote type="cite"
cite="mid:d406bbfce8694ea682a1d15a6bbfac01@mssm.edu">
<meta http-equiv="Content-Type" content="text/html;
charset=windows-1252">
<style type="text/css" style="display:none;"><!-- P {margin-top:0;margin-bottom:0;} --></style>
<div id="divtagdefaultwrapper"
style="font-size:10pt;color:#000000;font-family:Arial,Helvetica,sans-serif;"
dir="ltr">
<p>Thanks Irina,</p>
<p><br>
</p>
<p>Regarding the counting of the overlapped transcripts and
regulatory features (using stats_html), should I just count
how many times the string "transcript" or "regulatory
features" appears in the 'Feature' column?
<br>
</p>
<p>Also, what string would I be searching for in the
'Feature_type' column? In an example VEP annotated VCF, the
only relevant string was: '<span>sense_overlapping</span>'</p>
<p><br>
</p>
<p>Best regards,</p>
<p><br>
</p>
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font-size:14pt"><b><span
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font-size:10pt">Margaret Linan, MPH MS</span></b></span><b><span
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<div id="divRplyFwdMsg" dir="ltr"><font style="font-size:11pt"
face="Calibri, sans-serif" color="#000000"><b>From:</b> Irina
Armean <a class="moz-txt-link-rfc2396E" href="mailto:iarmean@ebi.ac.uk"><iarmean@ebi.ac.uk></a><br>
<b>Sent:</b> Monday, September 16, 2019 8:22:53 AM<br>
<b>To:</b> Ensembl developers list; Linan, Margaret<br>
<b>Subject:</b> Re: [ensembl-dev] VEP command line</font>
<div> </div>
</div>
<div>
<table width="200" cellspacing="0" border="1" bgcolor="yellow"
align="center">
<tbody>
<tr>
<td nowrap="nowrap">USE CAUTION: External Message.</td>
</tr>
</tbody>
</table>
<div>
<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">
<style type="text/css" style="display:none;"><!-- P {margin-top:0;margin-bottom:0;} --></style>
<div id="divtagdefaultwrapper"
style="font-size:10pt;color:#000000;font-family:Arial,Helvetica,sans-serif;"
dir="ltr">
<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>
<br>
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