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<p class="MsoNormal">Hi Ben,<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Thanks for your message!<o:p></o:p></p>
<p class="MsoNormal">Do you mean that the human haploid genome size 3,099,750,718 is the average or median size of male and female haploid genome?<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Thanks,<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Bin Xu, PhD<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
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<div style="border:none;border-top:solid #E1E1E1 1.0pt;padding:3.0pt 0in 0in 0in">
<p class="MsoNormal"><b>From:</b> Dev <dev-bounces@ensembl.org> <b>On Behalf Of </b>
Benjamin Moore<br>
<b>Sent:</b> Monday, December 11, 2023 6:50 AM<br>
<b>To:</b> dev@ensembl.org<br>
<b>Subject:</b> Re: [ensembl-dev] ***SPAM*** RE: REVEL Pluging in VEP 110<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
<p>Hi Bin Xu,<o:p></o:p></p>
<p>The genome size quoted on the species-specific hompages on the Ensembl websites refers to the length of the haploid genome size for that species, in the case of human, including sequences from both the X and Y chromosome. The genome assembly was generated
by the Genome Reference Consortium (GRC). You can read more about the genome assemblies and associated data/methods on the documentation:<o:p></o:p></p>
<p><a href="https://www.ncbi.nlm.nih.gov/grc/human">https://www.ncbi.nlm.nih.gov/grc/human</a><o:p></o:p></p>
<p>Best wishes<o:p></o:p></p>
<p>Ben<o:p></o:p></p>
<div>
<p class="MsoNormal">On 08/12/2023 17:24, Bin Xu wrote:<o:p></o:p></p>
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<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<p class="MsoPlainText">Dear Ensembl Team,<o:p></o:p></p>
<p class="MsoPlainText"> <o:p></o:p></p>
<p class="MsoPlainText">I am looking at the human genome size in your web page below, but it does not specify the base pairs 3,099,750,718 as either male, or female, or average of male and female.<o:p></o:p></p>
<p class="MsoPlainText">The same are the other species. As I know the female genome size is about 1.6% more than male.<o:p></o:p></p>
<p class="MsoPlainText">Could you please help to update the data by presenting female and male genome size respectively.<o:p></o:p></p>
<p class="MsoPlainText"> <o:p></o:p></p>
<p class="MsoPlainText"><a href="https://useast.ensembl.org/Homo_sapiens/Info/Annotation">https://useast.ensembl.org/Homo_sapiens/Info/Annotation</a><o:p></o:p></p>
<p class="MsoPlainText"><span style="mso-ligatures:none"><img border="0" width="609" height="291" style="width:6.3472in;height:3.0277in" id="Picture_x0020_1" src="cid:image001.png@01DA2C17.869606E0"></span><o:p></o:p></p>
<p class="MsoPlainText"> <o:p></o:p></p>
<p class="MsoPlainText">Best regards,<o:p></o:p></p>
<p class="MsoPlainText"> <o:p></o:p></p>
<p class="MsoPlainText"> <o:p></o:p></p>
<p class="MsoPlainText">Bin Xu, PhD <o:p></o:p></p>
<p class="MsoPlainText">Vice President<o:p></o:p></p>
<p class="MsoPlainText">O: 732-783-7398 | C: 267-318-5247<o:p></o:p></p>
<p class="MsoPlainText"><a href="mailto:bin.xu@accurantbiotech.com">bin.xu@accurantbiotech.com</a>
<o:p></o:p></p>
<p class="MsoPlainText">259 Prospect Plains Rd, Cranbury, NJ 08512<o:p></o:p></p>
<p class="MsoPlainText"> <o:p></o:p></p>
<p class="MsoPlainText"> <o:p></o:p></p>
<p class="MsoPlainText"> <o:p></o:p></p>
<p class="MsoPlainText"> <o:p></o:p></p>
<p class="MsoPlainText"> <o:p></o:p></p>
<p class="MsoPlainText">-----Original Message-----<br>
From: Dev <a href="mailto:dev-bounces@ensembl.org"><dev-bounces@ensembl.org></a> On Behalf Of Diana Lemos<br>
Sent: Friday, December 8, 2023 4:44 AM<br>
To: Souhila Amanzougarene <a href="mailto:souhila.amanzougarene@cnrs.fr"><souhila.amanzougarene@cnrs.fr></a><br>
Cc: Ensembl developers list <a href="mailto:dev@ensembl.org"><dev@ensembl.org></a><br>
Subject: Re: [ensembl-dev] REVEL Pluging in VEP 110<o:p></o:p></p>
<p class="MsoPlainText"> <o:p></o:p></p>
<p class="MsoPlainText">Hi,<o:p></o:p></p>
<p class="MsoPlainText"> <o:p></o:p></p>
<p class="MsoPlainText">The plugin was updated after release 108 which could have caused differences in the output.<o:p></o:p></p>
<p class="MsoPlainText"> <o:p></o:p></p>
<p class="MsoPlainText">Can you please send an example of your input file with variants that were expected to have a REVEL score but didn't with version 110?<o:p></o:p></p>
<p class="MsoPlainText"> <o:p></o:p></p>
<p class="MsoPlainText">Also, when did you download the REVEL file?<o:p></o:p></p>
<p class="MsoPlainText"> <o:p></o:p></p>
<p class="MsoPlainText"> <o:p></o:p></p>
<p class="MsoPlainText"> <o:p></o:p></p>
<p class="MsoPlainText"> <o:p></o:p></p>
<p class="MsoPlainText">On 08/12/2023 08:15, Souhila Amanzougarene wrote:<o:p></o:p></p>
<p class="MsoPlainText">> Dear Ensembl Team,<o:p></o:p></p>
<p class="MsoPlainText">> <o:p></o:p></p>
<p class="MsoPlainText">> I'm using VEP tool version 110 to annotate a VCF file (hg38) with the
<o:p></o:p></p>
<p class="MsoPlainText">> REVEL plugin. I processed it by running the following command :<o:p></o:p></p>
<p class="MsoPlainText">> <o:p></o:p></p>
<p class="MsoPlainText">> ./vep -i variations.vcf --assembly GRCh38 --plugin <o:p>
</o:p></p>
<p class="MsoPlainText">> REVEL,file=/path/to/revel/data.tsv.gz<o:p></o:p></p>
<p class="MsoPlainText">> <o:p></o:p></p>
<p class="MsoPlainText">> This command runs without any errors, but the REVEL column is empty in
<o:p></o:p></p>
<p class="MsoPlainText">> the annotated VCF.<o:p></o:p></p>
<p class="MsoPlainText">> <o:p></o:p></p>
<p class="MsoPlainText">> I attempted to run VEP 110 using the REVEL.pm file from VEP 108, and
<o:p></o:p></p>
<p class="MsoPlainText">> it worked, I now have scores in the REVEL column.<o:p></o:p></p>
<p class="MsoPlainText">> <o:p></o:p></p>
<p class="MsoPlainText">> <o:p></o:p></p>
<p class="MsoPlainText">> Thak you for your assisatnce !<o:p></o:p></p>
<p class="MsoPlainText">> <o:p></o:p></p>
<p class="MsoPlainText">> Best regards,<o:p></o:p></p>
<p class="MsoPlainText">> <o:p></o:p></p>
<p class="MsoPlainText"> <o:p></o:p></p>
<p class="MsoPlainText">_______________________________________________<o:p></o:p></p>
<p class="MsoPlainText">Dev mailing list <a href="mailto:Dev@ensembl.org"><span style="color:windowtext;text-decoration:none">Dev@ensembl.org</span></a><o:p></o:p></p>
<p class="MsoPlainText">Posting guidelines and subscribe/unsubscribe info: <a href="https://lists.ensembl.org/mailman/listinfo/dev_ensembl.org">
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<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>
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<pre>Ensembl Blog: <a href="http://www.ensembl.info/">http://www.ensembl.info/</a><o:p></o:p></pre>
</blockquote>
<pre>-- <o:p></o:p></pre>
<pre>Dr. Ben Moore (he/him)<o:p></o:p></pre>
<pre>Ensembl Outreach Manager<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre>European Bioinformatics Institute (EMBL-EBI)<o:p></o:p></pre>
<pre>European Molecular Biology Laboratory<o:p></o:p></pre>
<pre>Wellcome Trust Genome Campus<o:p></o:p></pre>
<pre>Hinxton<o:p></o:p></pre>
<pre>Cambridge<o:p></o:p></pre>
<pre>CB10 1SD<o:p></o:p></pre>
<pre>UK<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre><a href="mailto:bmoore@ebi.ac.uk">bmoore@ebi.ac.uk</a><o:p></o:p></pre>
<pre>+44 (0)1223 494265<o:p></o:p></pre>
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