<html xmlns:v="urn:schemas-microsoft-com:vml" xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="urn:schemas-microsoft-com:office:word" xmlns:m="http://schemas.microsoft.com/office/2004/12/omml" xmlns="http://www.w3.org/TR/REC-html40">
<head>
<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
<meta name="Generator" content="Microsoft Word 15 (filtered medium)">
<style><!--
/* Font Definitions */
@font-face
{font-family:"Cambria Math";
panose-1:2 4 5 3 5 4 6 3 2 4;}
@font-face
{font-family:Calibri;
panose-1:2 15 5 2 2 2 4 3 2 4;}
@font-face
{font-family:Consolas;
panose-1:2 11 6 9 2 2 4 3 2 4;}
/* Style Definitions */
p.MsoNormal, li.MsoNormal, div.MsoNormal
{margin:0in;
margin-bottom:.0001pt;
font-size:11.0pt;
font-family:"Calibri",sans-serif;
color:black;}
a:link, span.MsoHyperlink
{mso-style-priority:99;
color:blue;
text-decoration:underline;}
pre
{mso-style-priority:99;
mso-style-link:"HTML Preformatted Char";
margin:0in;
margin-bottom:.0001pt;
font-size:10.0pt;
font-family:"Courier New";
color:black;}
span.HTMLPreformattedChar
{mso-style-name:"HTML Preformatted Char";
mso-style-priority:99;
mso-style-link:"HTML Preformatted";
font-family:Consolas;
color:black;}
span.EmailStyle23
{mso-style-type:personal-compose;
font-family:"Calibri",sans-serif;
color:windowtext;}
.MsoChpDefault
{mso-style-type:export-only;
font-size:10.0pt;}
@page WordSection1
{size:8.5in 11.0in;
margin:1.0in 1.0in 1.0in 1.0in;}
div.WordSection1
{page:WordSection1;}
--></style><!--[if gte mso 9]><xml>
<o:shapedefaults v:ext="edit" spidmax="1026" />
</xml><![endif]--><!--[if gte mso 9]><xml>
<o:shapelayout v:ext="edit">
<o:idmap v:ext="edit" data="1" />
</o:shapelayout></xml><![endif]-->
</head>
<body bgcolor="white" lang="EN-US" link="blue" vlink="purple">
<div class="WordSection1">
<p class="MsoNormal"><span style="color:windowtext">Hi Souhila,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:windowtext"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color:windowtext"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color:windowtext">Thanks, that worked. But there is still missing data for the other columns, what can I do to fix this? Please see my attached annotated file.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:windowtext"><o:p> </o:p></span></p>
<p class="MsoNormal"><b><u>Here is my command</u></b>:<o:p></o:p></p>
<p class="MsoNormal">./vep -i ./project_data/top200k.vcf --tab --assembly GRCh38 --cache --offline --dir_plugins /root/.vep/Plugins --plugin CADD,./project_data/whole_genome_SNVs.tsv.gz,./project_data/InDels.tsv.gz -o annotations.vcf --everything --variant_class
--sift b --polyphen b --ccds --uniprot --hgvs --symbol --numbers --domains --regulatory --canonical --protein --biotype --uniprot --tsl --appris --gene_phenotype --af --af_1kg --af_esp --af_gnomad --max_af --pubmed --variant_class –mane<o:p></o:p></p>
<p class="MsoNormal"><span style="color:windowtext"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color:windowtext">Best,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:windowtext">Margaret<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:windowtext"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color:windowtext"><o:p> </o:p></span></p>
<div>
<div style="border:none;border-top:solid #E1E1E1 1.0pt;padding:3.0pt 0in 0in 0in">
<p class="MsoNormal"><b><span style="color:windowtext">From:</span></b><span style="color:windowtext"> Souhila Amanzougarene <souhila.amanzougarene@cnrs.fr>
<br>
<b>Sent:</b> Wednesday, April 8, 2020 12:46 AM<br>
<b>To:</b> Ensembl developers list <dev@ensembl.org>; Linan, Margaret <margaret.linan@mssm.edu><br>
<b>Subject:</b> Re: [ensembl-dev] CADD_RAW is SNV<o:p></o:p></span></p>
</div>
</div>
<p class="MsoNormal"><o:p> </o:p></p>
<div align="center">
<table class="MsoNormalTable" border="1" cellspacing="0" cellpadding="0" width="200" style="width:150.0pt;background:yellow">
<tbody>
<tr>
<td nowrap="" style="padding:.75pt .75pt .75pt .75pt">
<p class="MsoNormal">USE CAUTION: External Message.<o:p></o:p></p>
</td>
</tr>
</tbody>
</table>
</div>
<div>
<p>Hi Margaret,<o:p></o:p></p>
<p>You obtain SNV in the CADD_RAW column, because you have using the file : whole_genome_SNVs_inclAnno.tsv.gz instead of : whole_genome_SNVs.tsv.gz that contains CADD score.<o:p></o:p></p>
<p>CADD plugin only reports scores and does not consider any additional annotations from a CADD file. It is therefore sufficient to use CADD files without the additional annotations.
<o:p></o:p></p>
<p>Hope this helps<o:p></o:p></p>
<p>Best regards<o:p></o:p></p>
<p>Souhila<o:p></o:p></p>
<div>
<p class="MsoNormal">Le 07/04/2020 à 22:55, Linan, Margaret a écrit :<o:p></o:p></p>
</div>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<p class="MsoNormal">Hi –<o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoNormal">I am trying to use vep in tab delimited mode. But no matter what I do, I keep seeing SNV in the CADD_RAW column.
<o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoNormal"><b><u>Here is my command</u></b>:<o:p></o:p></p>
<p class="MsoNormal">./vep -i ./project_data/top200k.vcf --tab --assembly GRCh38 --cache --offline --dir_plugins /root/.vep/Plugins --plugin CADD,./project_data/whole_genome_SNVs_in<o:p></o:p></p>
<p class="MsoNormal">clAnno.tsv.gz,./project_data/InDels_inclAnno.tsv.gz -o annotations.vcf --everything --variant_class --sift b --polyphen b --ccds --uniprot --hgvs --symbol --num<o:p></o:p></p>
<p class="MsoNormal">bers --domains --regulatory --canonical --protein --biotype --uniprot --tsl --appris --gene_phenotype --af --af_1kg --af_esp --af_gnomad --max_af --pubmed --var<o:p></o:p></p>
<p class="MsoNormal">iant_class –mane<o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoNormal">Best,<o:p></o:p></p>
<p class="MsoNormal">Margaret<o:p></o:p></p>
<p class="MsoNormal"><br>
<br>
<o:p></o:p></p>
<pre>_______________________________________________<o:p></o:p></pre>
<pre>Dev mailing list <a href="mailto:Dev@ensembl.org">Dev@ensembl.org</a><o:p></o:p></pre>
<pre>Posting guidelines and subscribe/unsubscribe info: <a href="https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.ensembl.org_mailman_listinfo_dev-5Fensembl.org&d=DwMD-g&c=shNJtf5dKgNcPZ6Yh64b-A&r=kRxZpbitOhDkEC3BuUN1vDtzo3iicYrRn6woDJL_jnA&m=aB-9z7RzWEP4a5q1iyIMZ8bquwo0gX2YfgEe_6JouXo&s=GCqALYOFHFwecOGJ-WNwUP0fyhG7YAdTuMfWtfv9TrM&e=">https://lists.ensembl.org/mailman/listinfo/dev_ensembl.org</a><o:p></o:p></pre>
<pre>Ensembl Blog: <a href="https://urldefense.proofpoint.com/v2/url?u=http-3A__www.ensembl.info_&d=DwMD-g&c=shNJtf5dKgNcPZ6Yh64b-A&r=kRxZpbitOhDkEC3BuUN1vDtzo3iicYrRn6woDJL_jnA&m=aB-9z7RzWEP4a5q1iyIMZ8bquwo0gX2YfgEe_6JouXo&s=VWKFwIuEkxWVU62Zw6hsZlqPusmbkRjUcS4c6SkesCA&e=">http://www.ensembl.info/</a><o:p></o:p></pre>
</blockquote>
</div>
</div>
</body>
</html>