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<p>Hi Bin Xu,</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:</p>
<p><a class="moz-txt-link-freetext" href="https://www.ncbi.nlm.nih.gov/grc/human">https://www.ncbi.nlm.nih.gov/grc/human</a><br>
</p>
<p>Best wishes</p>
<p>Ben<br>
</p>
<div class="moz-cite-prefix">On 08/12/2023 17:24, Bin Xu wrote:<br>
</div>
<blockquote type="cite"
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<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"
moz-do-not-send="true" class="moz-txt-link-freetext">https://useast.ensembl.org/Homo_sapiens/Info/Annotation</a><o:p></o:p></p>
<p class="MsoPlainText"><o:p></o:p></p>
<p class="MsoPlainText"><img
style="width:6.3402in;height:3.0277in" id="Picture_x0020_1"
src="cid:part1.AHBeHbNC.9NhRXOOH@ebi.ac.uk" class=""
width="609" height="291" border="0"><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"
moz-do-not-send="true" class="moz-txt-link-freetext">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 class="moz-txt-link-rfc2396E" 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 class="moz-txt-link-rfc2396E" href="mailto:souhila.amanzougarene@cnrs.fr"><souhila.amanzougarene@cnrs.fr></a><br>
Cc: Ensembl developers list <a class="moz-txt-link-rfc2396E" href="mailto:dev@ensembl.org"><dev@ensembl.org></a><br>
Subject: Re: [ensembl-dev] REVEL Pluging in VEP 110</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
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<pre class="moz-signature" cols="72">--
Dr. Ben Moore (he/him)
Ensembl Outreach Manager
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge
CB10 1SD
UK
<a class="moz-txt-link-abbreviated" href="mailto:bmoore@ebi.ac.uk">bmoore@ebi.ac.uk</a>
+44 (0)1223 494265</pre>
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