[ensembl-dev] ***SPAM*** RE: REVEL Pluging in VEP 110
Benjamin Moore
bmoore at ebi.ac.uk
Mon Dec 11 16:45:38 GMT 2023
Hi Bin,
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).
I hope this helps.
Best wishes
Ben
On 11/12/2023 16:38, Bin Xu wrote:
>
> 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
> *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
>
> 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>
> <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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>
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> Ensembl Blog:http://www.ensembl.info/
>
> --
>
> 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
>
>
>
> _______________________________________________
>
> Dev mailing listDev at ensembl.org
>
> Posting guidelines and subscribe/unsubscribe info:https://lists.ensembl.org/mailman/listinfo/dev_ensembl.org
>
> Ensembl Blog:http://www.ensembl.info/
>
> --
> 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
>
> _______________________________________________
> Dev mailing listDev at ensembl.org
> Posting guidelines and subscribe/unsubscribe info:https://lists.ensembl.org/mailman/listinfo/dev_ensembl.org
> Ensembl Blog:http://www.ensembl.info/
--
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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