<div dir="ltr">Thanks for the comprehensive answer.<div><br></div><div>G.</div></div><div class="gmail_extra"><br><div class="gmail_quote">On 20 April 2016 at 13:52, Will McLaren <span dir="ltr"><<a href="mailto:wm2@ebi.ac.uk" target="_blank">wm2@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"><div dir="ltr">Hello,<div><br></div><div>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.</div><div><br></div><div>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.</div><div><br></div><div>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.</div><div><br></div><div>Have a read through the documentation [1] (especially the fields we produce in the output [2]).</div><div><br></div><div>Hope that helps</div><div><br></div><div>Will McLaren</div><div>Ensembl Variation</div><div><br></div><div>[1] : <a href="http://www.ensembl.org/info/docs/tools/vep/index.html" target="_blank">http://www.ensembl.org/info/docs/tools/vep/index.html</a></div><div>[2] : <a href="http://www.ensembl.org/info/docs/tools/vep/vep_formats.html#output" target="_blank">http://www.ensembl.org/info/docs/tools/vep/vep_formats.html#output</a></div></div><div class="HOEnZb"><div class="h5"><div class="gmail_extra"><br><div class="gmail_quote">On 19 April 2016 at 21:07, Genomeo Dev <span dir="ltr"><<a href="mailto:genomeodev@gmail.com" target="_blank">genomeodev@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><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><span><font color="#888888"><div><br></div></font></span><div><span><font color="#888888">G.</font></span><div><div><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><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>
> 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" rel="noreferrer" target="_blank">http://lists.ensembl.org/mailman/listinfo/dev</a><br>
> Ensembl Blog: <a href="http://www.ensembl.info/" rel="noreferrer" target="_blank">http://www.ensembl.info/</a><br>
<br>
<br>
_______________________________________________<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" rel="noreferrer" target="_blank">http://lists.ensembl.org/mailman/listinfo/dev</a><br>
Ensembl Blog: <a href="http://www.ensembl.info/" rel="noreferrer" target="_blank">http://www.ensembl.info/</a><br>
</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
</div>
<br></div></div><br>_______________________________________________<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" rel="noreferrer" target="_blank">http://lists.ensembl.org/mailman/listinfo/dev</a><br>
Ensembl Blog: <a href="http://www.ensembl.info/" rel="noreferrer" target="_blank">http://www.ensembl.info/</a><br>
<br></blockquote></div><br><br clear="all"><div><br></div>-- <br><div><div dir="ltr">G.</div></div>
</div></div></div></div></div>
<br>_______________________________________________<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" rel="noreferrer" target="_blank">http://lists.ensembl.org/mailman/listinfo/dev</a><br>
Ensembl Blog: <a href="http://www.ensembl.info/" rel="noreferrer" target="_blank">http://www.ensembl.info/</a><br>
<br></blockquote></div><br></div>
</div></div><br>_______________________________________________<br>
Dev mailing list <a href="mailto:Dev@ensembl.org">Dev@ensembl.org</a><br>
Posting guidelines and subscribe/unsubscribe info: <a href="http://lists.ensembl.org/mailman/listinfo/dev" rel="noreferrer" target="_blank">http://lists.ensembl.org/mailman/listinfo/dev</a><br>
Ensembl Blog: <a href="http://www.ensembl.info/" rel="noreferrer" target="_blank">http://www.ensembl.info/</a><br>
<br></blockquote></div><br><br clear="all"><div><br></div>-- <br><div class="gmail_signature"><div dir="ltr">G.</div></div>
</div>