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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">I see, Thanks!<o:p></o:p></p>
<p class="MsoNormal">I believe that the 22+X+Y size is accurate since your website is keeping updating it.<o:p></o:p></p>
<p class="MsoNormal">Could you please tell me where I can find the exact size of X chromosome and Y chromosome that your website refers to?<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<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 11:46 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>
</div>
</div>
<p class="MsoNormal"><o:p> </o:p></p>
<p>Hi Bin,<o:p></o:p></p>
<p>Yes, it is true thast the haploid male and female genome sizes are different. However, the reference human genome sequence is not a 'male' or 'female' genome sequence. Instead it contains all autosomes, plus both sex chromosomes. So, the genome size quoted
on the Ensembl site is the total of all 24 chromosomes (1-22 +X + Y).<o:p></o:p></p>
<p>I hope this helps.<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 11/12/2023 16:38, Bin Xu wrote:<o:p></o:p></p>
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<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<p class="MsoNormal">Hi Ben,<o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoNormal">The haploid genome sizes of male and female are different, since X chromosome is longer than Y.<o:p></o:p></p>
<p class="MsoNormal">This is why I interpret that human haploid genome size 3,099,750,718 is the average.<o:p></o:p></p>
<p class="MsoNormal">Could you explain if I am wrong?<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<o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal"><b>From:</b> Dev <a href="mailto:dev-bounces@ensembl.org"><dev-bounces@ensembl.org></a>
<b>On Behalf Of </b>Benjamin Moore<br>
<b>Sent:</b> Monday, December 11, 2023 10:17 AM<br>
<b>To:</b> <a href="mailto:dev@ensembl.org">dev@ensembl.org</a><br>
<b>Subject:</b> Re: [ensembl-dev] ***SPAM*** RE: REVEL Pluging in VEP 110<o:p></o:p></p>
</div>
</div>
<p class="MsoNormal"> <o:p></o:p></p>
<p>Hi Bin Xu,<o:p></o:p></p>
<p>The human reference genome is a composite genome, derived from the sequence of several different anonymous individuals. The size is not an average, but a total of all chromosomal sequence (autosomes, plus X and Y).<o:p></o:p></p>
<p>More information can be found on the following pages:<o:p></o:p></p>
<p><a href="https://www.ncbi.nlm.nih.gov/grc/help/faq/#human-reference-genome-individuals">https://www.ncbi.nlm.nih.gov/grc/help/faq/#human-reference-genome-individuals</a><o:p></o:p></p>
<p>Best wishes<o:p></o:p></p>
<p>Ben<o:p></o:p></p>
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<p class="MsoNormal">On 11/12/2023 14:50, Bin Xu wrote:<o:p></o:p></p>
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<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<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 <a href="mailto:dev-bounces@ensembl.org"><dev-bounces@ensembl.org></a>
<b>On Behalf Of </b>Benjamin Moore<br>
<b>Sent:</b> Monday, December 11, 2023 6:50 AM<br>
<b>To:</b> <a href="mailto:dev@ensembl.org">dev@ensembl.org</a><br>
<b>Subject:</b> Re: [ensembl-dev] ***SPAM*** RE: REVEL Pluging in VEP 110<o:p></o:p></p>
</div>
</div>
<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>
</div>
<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@01DA2C28.CBD440D0"></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>
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<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>
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<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>
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<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>
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