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

[Genomeo Dev]

Thanks for the comprehensive answer.

G.

On 20 April 2016 at 13:52, Will McLaren <wm2 at ebi.ac.uk> wrote:

> 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
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>>>>
>>>>
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>>>
>>>
>>>
>>> --
>>> G.
>>> _______________________________________________
>>> Dev mailing list    Dev at ensembl.org
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>>>
>>>
>>> ---
>>> 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
>>>
>>>
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>>> Ensembl Blog: http://www.ensembl.info/
>>>
>>>
>>
>>
>> --
>> G.
>>
>> _______________________________________________
>> Dev mailing list    Dev at ensembl.org
>> Posting guidelines and subscribe/unsubscribe info:
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>> Ensembl Blog: http://www.ensembl.info/
>>
>>
>
> _______________________________________________
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>
>


-- 
G.
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