<html><head><meta http-equiv="Content-Type" content="text/html charset=us-ascii"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Hi Genomeo,<div class=""><br class=""></div><div class="">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. </div><div class=""><br class=""></div><div class="">More at <a href="http://genomeref.blogspot.co.uk/2013/12/announcing-grch38.html" class="">http://genomeref.blogspot.co.uk/2013/12/announcing-grch38.html</a> and <a href="http://genomeref.blogspot.co.uk/2014/01/grch38-incorporating-modeled-centromere.html" class="">http://genomeref.blogspot.co.uk/2014/01/grch38-incorporating-modeled-centromere.html</a></div><div class=""><br class=""></div><div class="">Best,</div><div class=""><br class=""></div><div class="">Kerstin</div><div class=""><br class=""></div><div class=""><br class=""><div><blockquote type="cite" class=""><div class="">On 19 Apr 2016, at 11:14, Genomeo Dev <<a href="mailto:genomeodev@gmail.com" class="">genomeodev@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class="">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.<div class=""><br class=""></div><div class="">G.</div></div><div class="gmail_extra"><br class=""><div class="gmail_quote">On 19 April 2016 at 12:51, Thibaut Hourlier <span dir="ltr" class=""><<a href="mailto:thibaut@ebi.ac.uk" target="_blank" class="">thibaut@ebi.ac.uk</a>></span> wrote:<br class=""><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi Genomeo,<br class="">
You should use GRCh38 as it is an improved version of GRCh37<br class="">
<br class="">
What exactly do you want to annotate?<br class="">
<br class="">
Thanks<br class="">
Thibaut<br class="">
<div class=""><div class="h5"><br class="">
> On 19 Apr 2016, at 10:30, Genomeo Dev <<a href="mailto:genomeodev@gmail.com" class="">genomeodev@gmail.com</a>> wrote:<br class="">
><br class="">
> Dear all,<br class="">
><br class="">
> 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.<br class="">
><br class="">
> 1) Would you recommend to go for GRCH37 or GRCH38?<br class="">
><br class="">
> 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.<br class="">
><br class="">
> Thank you,<br class="">
><br class="">
> --<br class="">
> G.<br class="">
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</blockquote></div><br class=""><br clear="all" class=""><div class=""><br class=""></div>-- <br class=""><div class="gmail_signature"><div dir="ltr" class="">G.</div></div>
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---<br class="">Dr. Kerstin Howe<br class="">Senior Scientific Manager<br class="">Genome Reference Informatics<br class=""><a href="mailto:kerstin@sanger.ac.uk" class="">kerstin@sanger.ac.uk</a><br class="">orcid.org/0000-0003-2237-513X<br class=""><br class="">Wellcome Trust Sanger Institute<br class="">Hinxton, Cambridge CB10 1SA, UK
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