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<p>Hi Margaret,</p>
<p><br>
</p>
<p>just to clarify, there is no stats_html command. VEP will collect
and write the summary data to the summary file at the same time it
annotates and writes the results to the results file.<br>
</p>
<p><br>
</p>
<p>The fields "Variants Processed" in the summary html file
represents the total number of variants that were read.</p>
<p>I assume by "Variants remaining after filtering" you mean
"Variants filtered out", This count represents any input variants
that were filtered out due to using the VEP --freq_filter and
--freq_freq options (filters on allele frequency).<br>
</p>
<p><br>
</p>
<p>The same VEP command will process all VCFs the same. There are
multiple options to filter and do QC using VEP and they are
described on the following page: <a
href="https://www.ensembl.org/info/docs/tools/vep/script/vep_options.html#filt">https://www.ensembl.org/info/docs/tools/vep/script/vep_options.html#filt</a></p>
<p> </p>
<p><br>
</p>
<p>Kind regards,</p>
<p>Irina<br>
</p>
<p><br>
</p>
<div class="moz-cite-prefix">On 17/09/2019 22:51, Linan, Margaret
wrote:<br>
</div>
<blockquote type="cite"
cite="mid:94da34b575df45f2a3823d5e62c1399a@mssm.edu">
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<p>Hi Irina,</p>
<p><br>
</p>
<p>Thanks, also I forgot to ask, regarding the stats_html
command, there are two fields in the output html "Variants
Processed' and 'Variants remaining after filtering'.</p>
<p><br>
</p>
<p>What processes are normally used to process and filter these
VCFs. Does VEP use the same processing approach for all VCFs?</p>
<p><br>
</p>
<p>Best Regards,<br>
</p>
<p><br>
</p>
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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> Tuesday, September 17, 2019 10:01:26 AM<br>
<b>To:</b> Linan, Margaret; Ensembl developers list<br>
<b>Subject:</b> Re: [ensembl-dev] VEP command line</font>
<div> </div>
</div>
<div>
<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,
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</span></p>
<p><span style="color: rgb(51, 51, 51); font-family: "Luxi
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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:
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!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:
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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">
<style type="text/css" style="display:none;"><!-- P {margin-top:0;margin-bottom:0;} --></style>
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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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<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" moz-do-not-send="true"><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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