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Hello<br>
<br>
Thanks for your reply. I have not received any emails from Rhoda or
Beth in relation to my original post about the extra table. Was
there perhaps a problem with the mailing list recently? I didn't
receive any messages for a couple of days but I assumed it was
Easter break. I seem to be getting them now again as I have received
your's and will's emails today.<br>
<br>
I Have searched the archives and can see the posts there though.<br>
<br>
cheers<br>
<br>
On 04/05/11 08:08, Pontus Larsson wrote:
<blockquote
cite="mid:BANLkTinLD+tpj4kNJkE_P+odGAzsWGGw0Q@mail.gmail.com"
type="cite">Hi Andrea,
<div><br>
</div>
<div>1. This is a production table that was mistakenly included in
the dump. Please see Rhoda and Beth's answers to your original
post.</div>
<div><br>
</div>
<div>2. I will leave it to Will to answer this fully but I believe
this has to do with the way indels are specified in the VCF file
format.</div>
<div><br>
</div>
<div>3. Since HGMD do not disclose the alleles of their variations
to us, we cannot merge HGMD variations with co-located
variations from dbSNP or any other source. Thus, these will be
listed as co-located (rather than synonyms) and will not mask or
replace dbSNP as the source of the variation.</div>
<div><br>
</div>
<div>Hope this helps</div>
<div>/Pontus</div>
<div><br>
<br>
<div class="gmail_quote">2011/5/4 Andrea Edwards <span
dir="ltr"><<a moz-do-not-send="true"
href="mailto:edwardsa@cs.man.ac.uk">edwardsa@cs.man.ac.uk</a>></span><br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
Hello<br>
<br>
I hope you all had a nice Easter break.<br>
<br>
I'd also like to express my appreciation for the work done
on the new variation api, documentation and VEP. It is
deeply enriched.<br>
<br>
I have a few quick questions if that is ok:<br>
<br>
1) The human and cow variation downloads for e!62 include
data for a table called mart_transcript_variation but the
definition for this table is not in the sql file. Neither is
this table mentioned on this page<br>
<br>
<a moz-do-not-send="true"
href="http://www.ensembl.org/info/docs/variation/variation_schema.html"
target="_blank">http://www.ensembl.org/info/docs/variation/variation_schema.html</a><br>
<br>
2) Did you see this comment on biostar about a possible
error in the VEP. I read through the VEP code and tend to
agree with the OP.<br>
<a moz-do-not-send="true"
href="http://biostar.stackexchange.com/questions/7781/problem-with-ensembl-variant-effect-predictor-stand-alone-perl-tool/7921#7921"
target="_blank">http://biostar.stackexchange.com/questions/7781/problem-with-ensembl-variant-effect-predictor-stand-alone-perl-tool/7921#7921</a><br>
<br>
3) If a variation is in dbSNP and HGMD will its source be
reported as HGMD? There are 57930 variations in the HGMD
variation set, and the same number of variations exist with
a source of HGMD so it seems HGMD would trump dbSNP as the
source of a variation.<br>
<br>
cheers<br>
<br>
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href="http://lists.ensembl.org/mailman/listinfo/dev"
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href="http://www.ensembl.info/" target="_blank">http://www.ensembl.info/</a><br>
</blockquote>
</div>
<br>
</div>
</blockquote>
<br>
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