[ensembl-dev] Genome build and annotator for new large scale WGS project

[Will McLaren]

Hello,

It really depends on what links you are intending to use. For the most part
snpEff and VEP perform a very similar function in terms of calling
functional consequences.

VEP is an Ensembl product so it would be fair to assume that any links into
Ensembl data will be more detailed/robust/up-to-date. VEP provides many
more external references for transcript annotations (e.g. linking Ensembl
IDs to UniProt or CCDS). VEP uses the Ensembl Variation database to
cross-check known variants against your input, which is probably the most
comprehensive available database of genomic variants and associated data.
VEP also provides more detailed annotations of the effects of variants on
regulatory elements.

snpEff does however have a performance advantage over VEP, so if it is just
the functional consequences you want (and quickly!) then snpEff would
perhaps be more suitable.

Have a read through the documentation [1] (especially the fields we produce
in the output [2]).

Hope that helps

Will McLaren
Ensembl Variation

[1] : http://www.ensembl.org/info/docs/tools/vep/index.html
[2] : http://www.ensembl.org/info/docs/tools/vep/vep_formats.html#output

On 19 April 2016 at 21:07, Genomeo Dev <genomeodev at gmail.com> wrote:

> Thanks very much.
>
> How about VEP, are there any advantages for choosing this compared to
> Snpeff? Especially in terms of linking to the various public data including
> Ensembl's.
>
> G.
>
>
> On 19 April 2016 at 14:51, Kerstin Howe <kj2 at sanger.ac.uk> wrote:
>
>> Hi Genomeo,
>>
>> In this case I would definitely recommend GRCh38. It contains the results
>> of more than 5 years of sequence improvements including the correction of
>> nearly 9000 single bp sequencing errors that would otherwise come up as
>> variation, and modelled centromere sequence as a nice read sink.
>>
>> More at http://genomeref.blogspot.co.uk/2013/12/announcing-grch38.html
>>  and
>> http://genomeref.blogspot.co.uk/2014/01/grch38-incorporating-modeled-centromere.html
>>
>> Best,
>>
>> Kerstin
>>
>>
>> On 19 Apr 2016, at 11:14, Genomeo Dev <genomeodev at gmail.com> wrote:
>>
>> Thanks. Aim is to annotate with the predicted functional consequences
>> based on what is publicly known about the genome annotation. Sort of what
>> you get from VEP.
>>
>> G.
>>
>> On 19 April 2016 at 12:51, Thibaut Hourlier <thibaut at ebi.ac.uk> wrote:
>>
>>> Hi Genomeo,
>>> You should use GRCh38 as it is an improved version of GRCh37
>>>
>>> What exactly do you want to annotate?
>>>
>>> Thanks
>>> Thibaut
>>>
>>> > On 19 Apr 2016, at 10:30, Genomeo Dev <genomeodev at gmail.com> wrote:
>>> >
>>> > Dear all,
>>> >
>>> > We are trying to generate whole genome sequences for 25,000 samples
>>> using short read data form Illumina. This will be used in many downstream
>>> analyses and other related projects.
>>> >
>>> > 1) Would you recommend to go for GRCH37 or GRCH38?
>>> >
>>> > 2) For the annotation, what are the main advantages to adopting VEP as
>>> the annotator tool? especially in linking with public databases and
>>> comparing to other genomics studies.
>>> >
>>> > Thank you,
>>> >
>>> > --
>>> > G.
>>> > _______________________________________________
>>> > Dev mailing list    Dev at ensembl.org
>>> > Posting guidelines and subscribe/unsubscribe info:
>>> http://lists.ensembl.org/mailman/listinfo/dev
>>> > Ensembl Blog: http://www.ensembl.info/
>>>
>>>
>>> _______________________________________________
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>>
>>
>>
>> --
>> G.
>> _______________________________________________
>> Dev mailing list    Dev at ensembl.org
>> Posting guidelines and subscribe/unsubscribe info:
>> http://lists.ensembl.org/mailman/listinfo/dev
>> Ensembl Blog: http://www.ensembl.info/
>>
>>
>> ---
>> Dr. Kerstin Howe
>> Senior Scientific Manager
>> Genome Reference Informatics
>> kerstin at sanger.ac.uk
>> orcid.org/0000-0003-2237-513X
>>
>> Wellcome Trust Sanger Institute
>> Hinxton, Cambridge CB10 1SA, UK
>>
>>
>> _______________________________________________
>> Dev mailing list    Dev at ensembl.org
>> Posting guidelines and subscribe/unsubscribe info:
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>> Ensembl Blog: http://www.ensembl.info/
>>
>>
>
>
> --
> G.
>
> _______________________________________________
> Dev mailing list    Dev at ensembl.org
> Posting guidelines and subscribe/unsubscribe info:
> http://lists.ensembl.org/mailman/listinfo/dev
> Ensembl Blog: http://www.ensembl.info/
>
>
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