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

Genomeo Dev genomeodev at gmail.com
Tue Apr 19 21:07:38 BST 2016


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.
>> > _______________________________________________
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>>
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>
>
>
> --
> G.
> _______________________________________________
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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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>


-- 
G.
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