[ensembl-dev] ***SPAM*** RE: REVEL Pluging in VEP 110

[Benjamin Moore]

Hi Bin Xu,

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:

https://www.ncbi.nlm.nih.gov/grc/human

Best wishes

Ben

On 08/12/2023 17:24, Bin Xu wrote:
>
> Dear Ensembl Team,
>
> 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.
>
> The same are the other species. As I know the female genome size is 
> about 1.6% more than male.
>
> Could you please help to update the data by presenting female and male 
> genome size respectively.
>
> https://useast.ensembl.org/Homo_sapiens/Info/Annotation
>
> Best regards,
>
> Bin Xu, PhD
>
> Vice President
>
> O: 732-783-7398 | C: 267-318-5247
>
> bin.xu at accurantbiotech.com
>
> 259 Prospect Plains Rd, Cranbury, NJ 08512
>
> -----Original Message-----
> From: Dev <dev-bounces at ensembl.org> On Behalf Of Diana Lemos
> Sent: Friday, December 8, 2023 4:44 AM
> To: Souhila Amanzougarene <souhila.amanzougarene at cnrs.fr>
> Cc: Ensembl developers list <dev at ensembl.org>
> Subject: Re: [ensembl-dev] REVEL Pluging in VEP 110
>
> Hi,
>
> The plugin was updated after release 108 which could have caused 
> differences in the output.
>
> 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?
>
> Also, when did you download the REVEL file?
>
> On 08/12/2023 08:15, Souhila Amanzougarene wrote:
>
> > Dear Ensembl Team,
>
> >
>
> > I'm using VEP tool version 110 to annotate a VCF file (hg38) with the
>
> > REVEL plugin. I processed it by running the following command :
>
> >
>
> > ./vep -i variations.vcf --assembly GRCh38 --plugin
>
> > REVEL,file=/path/to/revel/data.tsv.gz
>
> >
>
> > This command runs without any errors, but the REVEL column is empty in
>
> > the annotated VCF.
>
> >
>
> > I attempted to run VEP 110 using the REVEL.pm file from VEP 108, and
>
> > it worked, I now have scores in the REVEL column.
>
> >
>
> >
>
> > Thak you for your assisatnce !
>
> >
>
> > Best regards,
>
> >
>
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-- 
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

bmoore at ebi.ac.uk
+44 (0)1223 494265
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