<div dir="ltr">Thanks very much.<div><br></div><div>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.</div><div><br></div><div>G.<br><div class="gmail_extra"><br><div class="gmail_quote">On 19 April 2016 at 14:51, Kerstin Howe <span dir="ltr"><<a href="mailto:kj2@sanger.ac.uk" target="_blank">kj2@sanger.ac.uk</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="word-wrap:break-word">Hi Genomeo,<div><br></div><div>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><br></div><div>More at <a href="http://genomeref.blogspot.co.uk/2013/12/announcing-grch38.html" target="_blank">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" target="_blank">http://genomeref.blogspot.co.uk/2014/01/grch38-incorporating-modeled-centromere.html</a></div><div><br></div><div>Best,</div><div><br></div><div>Kerstin</div><div><br></div><div><div><div class="h5"><br><div><blockquote type="cite"><div>On 19 Apr 2016, at 11:14, Genomeo Dev <<a href="mailto:genomeodev@gmail.com" target="_blank">genomeodev@gmail.com</a>> wrote:</div><br><div><div dir="ltr">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><br></div><div>G.</div></div><div class="gmail_extra"><br><div class="gmail_quote">On 19 April 2016 at 12:51, Thibaut Hourlier <span dir="ltr"><<a href="mailto:thibaut@ebi.ac.uk" target="_blank">thibaut@ebi.ac.uk</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi Genomeo,<br>
You should use GRCh38 as it is an improved version of GRCh37<br>
<br>
What exactly do you want to annotate?<br>
<br>
Thanks<br>
Thibaut<br>
<div><div><br>
> On 19 Apr 2016, at 10:30, Genomeo Dev <<a href="mailto:genomeodev@gmail.com" target="_blank">genomeodev@gmail.com</a>> wrote:<br>
><br>
> Dear all,<br>
><br>
> 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>
><br>
> 1) Would you recommend to go for GRCH37 or GRCH38?<br>
><br>
> 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>
><br>
> Thank you,<br>
><br>
> --<br>
> G.<br>
</div></div>> _______________________________________________<br>
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</blockquote></div><br><br clear="all"><div><br></div>-- <br><div><div dir="ltr">G.</div></div>
</div>
_______________________________________________<br>Dev mailing list    <a href="mailto:Dev@ensembl.org" target="_blank">Dev@ensembl.org</a><br>Posting guidelines and subscribe/unsubscribe info: <a href="http://lists.ensembl.org/mailman/listinfo/dev" target="_blank">http://lists.ensembl.org/mailman/listinfo/dev</a><br>Ensembl Blog: <a href="http://www.ensembl.info/" target="_blank">http://www.ensembl.info/</a><br></div></blockquote></div><br></div></div><div>
---<br>Dr. Kerstin Howe<br>Senior Scientific Manager<br>Genome Reference Informatics<br><a href="mailto:kerstin@sanger.ac.uk" target="_blank">kerstin@sanger.ac.uk</a><br><a href="http://orcid.org/0000-0003-2237-513X" target="_blank">orcid.org/0000-0003-2237-513X</a><br><br>Wellcome Trust Sanger Institute<br>Hinxton, Cambridge CB10 1SA, UK

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<br></blockquote></div><br><br clear="all"><div><br></div>-- <br><div class="gmail_signature"><div dir="ltr">G.</div></div>
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