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

Mon Dec 11 16:38:14 GMT 2023

Hi Ben,

The haploid genome sizes of male and female are different, since X chromosome is longer than Y.
This is why I interpret that human haploid genome size 3,099,750,718 is the average.
Could you explain if I am wrong?

Thanks,

Bin

From: Dev <dev-bounces at ensembl.org> On Behalf Of Benjamin Moore
Sent: Monday, December 11, 2023 10:17 AM
To: dev at ensembl.org
Subject: Re: [ensembl-dev] ***SPAM*** RE: REVEL Pluging in VEP 110

Hi Bin Xu,

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).

More information can be found on the following pages:

https://www.ncbi.nlm.nih.gov/grc/help/faq/#human-reference-genome-individuals

Best wishes

Ben
On 11/12/2023 14:50, Bin Xu wrote:
Hi Ben,

Thanks for your message!
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?

Thanks,

Bin Xu, PhD

From: Dev <dev-bounces at ensembl.org><mailto:dev-bounces at ensembl.org> On Behalf Of Benjamin Moore
Sent: Monday, December 11, 2023 6:50 AM
To: dev at ensembl.org<mailto:dev at ensembl.org>
Subject: Re: [ensembl-dev] ***SPAM*** RE: REVEL Pluging in VEP 110

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

[cid:image001.png at 01DA2C26.8605FE10]

Best regards,

Bin Xu, PhD

Vice President

O: 732-783-7398 | C: 267-318-5247

bin.xu at accurantbiotech.com<mailto:bin.xu at accurantbiotech.com>

259 Prospect Plains Rd, Cranbury, NJ 08512

-----Original Message-----
From: Dev <dev-bounces at ensembl.org><mailto: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><mailto:souhila.amanzougarene at cnrs.fr>
Cc: Ensembl developers list <dev at ensembl.org><mailto: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

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UK

bmoore at ebi.ac.uk<mailto:bmoore at ebi.ac.uk>

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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<mailto:bmoore at ebi.ac.uk>

+44 (0)1223 494265
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