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

[Kerstin Howe]

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 <http://genomeref.blogspot.co.uk/2013/12/announcing-grch38.html> and http://genomeref.blogspot.co.uk/2014/01/grch38-incorporating-modeled-centromere.html <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 <mailto: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 <mailto: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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> 
> 
> -- 
> 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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