Hello Gavin,<div><br></div><div>We apply some QC checking to the data that we import - we can assign variations a status of "failed", along with a description of why this has happened. You can access this through a variation object using the failed_description() method. The list Andrea gave is the list of all possible failed descriptions.</div>
<div><br></div><div>The API is configured such that by default data associated with failed variations are not returned by methods that return more than one object (e.g. fetch_all_by_Slice in VariationFeatureAdaptor); you can force the retrieval of such data by retrieving the variation directly (e.g. using fetch_by_name in VariationAdaptor), or by calling the method include_failed_variations() on any adaptor from the Variation group (functionality only available from e!61 onwards).</div>
<div><br></div><div>Thanks</div><div><br></div><div>Will</div><div><br><br><div class="gmail_quote">On 7 February 2011 09:29, Oliver, Gavin <span dir="ltr"><<a href="mailto:gavin.oliver@almacgroup.com">gavin.oliver@almacgroup.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<div lang="EN-US" link="blue" vlink="blue">
<div>
<p class="MsoNormal"><font size="2" color="navy" face="Arial"><span style="font-size:10.0pt;font-family:Arial;color:navy">Those were the statuses I was referring to
Will.</span></font></p>
<p class="MsoNormal"><font size="2" color="navy" face="Arial"><span style="font-size:10.0pt;font-family:Arial;color:navy"> </span></font></p>
<p class="MsoNormal"><font size="2" color="navy" face="Arial"><span style="font-size:10.0pt;font-family:Arial;color:navy">Which leads me to ask – what were
the statuses that Andrea listed?</span></font></p>
<p class="MsoNormal"><font size="2" color="navy" face="Arial"><span style="font-size:10.0pt;font-family:Arial;color:navy"> </span></font></p>
<p class="MsoNormal"><font size="2" color="navy" face="Arial"><span style="font-size:10.0pt;font-family:Arial;color:navy">Gavin</span></font></p>
<p class="MsoNormal"><font size="2" color="navy" face="Arial"><span style="font-size:10.0pt;font-family:Arial;color:navy"> </span></font></p>
<div>
<div class="MsoNormal" align="center" style="text-align:center"><font size="3" face="Times New Roman"><span style="font-size:12.0pt">
<hr size="2" width="100%" align="center">
</span></font></div>
<p class="MsoNormal"><b><font size="2" face="Tahoma"><span style="font-size:10.0pt;font-family:Tahoma;font-weight:bold">From:</span></font></b><font size="2" face="Tahoma"><span style="font-size:10.0pt;font-family:Tahoma">
<a href="mailto:dev-bounces@ensembl.org" target="_blank">dev-bounces@ensembl.org</a> [mailto:<a href="mailto:dev-bounces@ensembl.org" target="_blank">dev-bounces@ensembl.org</a>] <b><span style="font-weight:bold">On Behalf Of </span></b>Will McLaren<br>
<b><span style="font-weight:bold">Sent:</span></b> 04 February 2011 15:04<br>
<b><span style="font-weight:bold">To:</span></b> Andrea Edwards<br>
<b><span style="font-weight:bold">Cc:</span></b> <a href="mailto:Dev@ensembl.org" target="_blank">Dev@ensembl.org</a><br>
<b><span style="font-weight:bold">Subject:</span></b> [SPAM] - Re:
[ensembl-dev] Transcript variation alleles - - Bayesian Filter detected spam</span></font></p>
</div>
<p class="MsoNormal"><font size="3" face="Times New Roman"><span style="font-size:12.0pt"> </span></font></p>
<p class="MsoNormal"><font size="3" face="Times New Roman"><span style="font-size:12.0pt">Hello,</span></font></p>
<div>
<p class="MsoNormal"><font size="3" face="Times New Roman"><span style="font-size:12.0pt"> </span></font></p>
</div>
<div>
<p class="MsoNormal"><font size="3" face="Times New Roman"><span style="font-size:12.0pt">I think there are some crossed wires here - validation_status is a
property of a variation supplied to us by dbSNP.</span></font></p>
</div>
<div>
<p class="MsoNormal"><font size="3" face="Times New Roman"><span style="font-size:12.0pt"> </span></font></p>
</div>
<div>
<p class="MsoNormal"><font size="3" face="Times New Roman"><span style="font-size:12.0pt">Their descriptions are here:</span></font></p>
</div>
<div>
<p class="MsoNormal"><font size="3" face="Times New Roman"><span style="font-size:12.0pt"> </span></font></p>
</div>
<div>
<p class="MsoNormal"><font size="3" face="Times New Roman"><span style="font-size:12.0pt"><a href="http://www.ncbi.nlm.nih.gov/projects/SNP/snp_legend.cgi?legend=validation" target="_blank">http://www.ncbi.nlm.nih.gov/projects/SNP/snp_legend.cgi?legend=validation</a><br>
<br>
The pictures are, in order:</span></font></p>
</div>
<div>
<p class="MsoNormal"><font size="3" face="Times New Roman"><span style="font-size:12.0pt"> </span></font></p>
</div>
<div>
<p class="MsoNormal"><font size="3" face="Times New Roman"><span style="font-size:12.0pt">cluster</span></font></p>
</div>
<div>
<p class="MsoNormal"><font size="3" face="Times New Roman"><span style="font-size:12.0pt">freq</span></font></p>
</div>
<div>
<p class="MsoNormal"><font size="3" face="Times New Roman"><span style="font-size:12.0pt">submitter</span></font></p>
</div>
<div>
<p class="MsoNormal"><font size="3" face="Times New Roman"><span style="font-size:12.0pt">doublehit</span></font></p>
</div>
<div>
<p class="MsoNormal"><font size="3" face="Times New Roman"><span style="font-size:12.0pt">hapmap</span></font></p>
</div>
<div>
<p class="MsoNormal"><font size="3" face="Times New Roman"><span style="font-size:12.0pt">1000Genome</span></font></p>
</div>
<div>
<p class="MsoNormal"><font size="3" face="Times New Roman"><span style="font-size:12.0pt"> </span></font></p>
</div>
<div>
<p class="MsoNormal" style="margin-bottom:12.0pt"><font size="3" face="Times New Roman"><span style="font-size:12.0pt">Will</span></font></p>
<div>
<p class="MsoNormal"><font size="3" face="Times New Roman"><span style="font-size:12.0pt">On 4 February 2011 14:14, Andrea Edwards <<a href="mailto:edwardsa@cs.man.ac.uk" target="_blank">edwardsa@cs.man.ac.uk</a>> wrote:</span></font></p>
<div text="#000000" bgcolor="#ffffff">
<p class="MsoNormal"><font size="3" face="Times New Roman"><span style="font-size:12.0pt"><br>
Gavin<br>
<br>
I believe the validatation statuses are just pass and fail <br>
<br>
If you query the variation schema directly you can find the reasons for failure
when a variation is imported from say dbSNP<br>
<br>
mysql> select description from failed_description;<br>
+--------------------------------------------------------+<br>
| description
|<br>
+--------------------------------------------------------+<br>
| Variation maps to more than 3 different
locations |<br>
| None of the variant alleles match the reference allele |<br>
| Variation has more than 3 different alleles
|<br>
| Loci with no observed variant alleles in
dbSNP |<br>
| Variation does not map to the
genome
|<br>
| Variation has no associated
sequence
|<br>
+--------------------------------------------------------+<br>
6 rows in set (0.06 sec)<br>
<br>
As will has said, they map all variants to the positive strand and make sure at
least one of the variant alleles exists at the base position in the forward
strand. If this failed you would get the error 'None of the variant alleles match
the reference allele.' I think the others are fairly self explanatory though
i'm not sure how a variant could have no associated sequence if it was imported
from dbSNP<br>
<br>
<br>
<br>
<br>
<br>
<br>
On 02/02/2011 15:20, Oliver, Gavin
wrote: </span></font></p>
<pre><font size="2" face="Courier New"><span style="font-size:10.0pt">Thanks Graham - </span></font></pre><pre><font size="2" face="Courier New"><span style="font-size:10.0pt"> </span></font></pre><pre><font size="2" face="Courier New"><span style="font-size:10.0pt">Can you also tell me where to find information on the meaning of the</span></font></pre>
<pre><font size="2" face="Courier New"><span style="font-size:10.0pt">possible validation statuses?</span></font></pre><pre><font size="2" face="Courier New"><span style="font-size:10.0pt"> </span></font></pre><pre><font size="2" face="Courier New"><span style="font-size:10.0pt"> </span></font></pre>
<pre><font size="2" face="Courier New"><span style="font-size:10.0pt"> </span></font></pre><pre><font size="2" face="Courier New"><span style="font-size:10.0pt">-----Original Message-----</span></font></pre><pre><font size="2" face="Courier New"><span style="font-size:10.0pt">From: Graham Ritchie [<a href="mailto:grsr@ebi.ac.uk" target="_blank">mailto:grsr@ebi.ac.uk</a>] </span></font></pre>
<pre><font size="2" face="Courier New"><span style="font-size:10.0pt">Sent: 02 February 2011 15:12</span></font></pre><pre><font size="2" face="Courier New"><span style="font-size:10.0pt">To: Oliver, Gavin</span></font></pre>
<pre><font size="2" face="Courier New"><span style="font-size:10.0pt">Cc: <a href="mailto:dev@ensembl.org" target="_blank">dev@ensembl.org</a></span></font></pre><pre><font size="2" face="Courier New"><span style="font-size:10.0pt">Subject: [SPAM] - Re: [ensembl-dev] Transcript variation alleles - Email</span></font></pre>
<pre><font size="2" face="Courier New"><span style="font-size:10.0pt">found in subject</span></font></pre><pre><font size="2" face="Courier New"><span style="font-size:10.0pt"> </span></font></pre><pre><font size="2" face="Courier New"><span style="font-size:10.0pt">Hi Gavin,</span></font></pre>
<pre><font size="2" face="Courier New"><span style="font-size:10.0pt"> </span></font></pre><pre><font size="2" face="Courier New"><span style="font-size:10.0pt">The alleles of a transcript variation always represent the genomic base</span></font></pre>
<pre><font size="2" face="Courier New"><span style="font-size:10.0pt">change.</span></font></pre><pre><font size="2" face="Courier New"><span style="font-size:10.0pt"> </span></font></pre><pre><font size="2" face="Courier New"><span style="font-size:10.0pt">Cheers,</span></font></pre>
<pre><font size="2" face="Courier New"><span style="font-size:10.0pt"> </span></font></pre><pre><font size="2" face="Courier New"><span style="font-size:10.0pt">Graham</span></font></pre><pre><font size="2" face="Courier New"><span style="font-size:10.0pt"> </span></font></pre>
<pre><font size="2" face="Courier New"><span style="font-size:10.0pt">Ensembl variation</span></font></pre><pre><font size="2" face="Courier New"><span style="font-size:10.0pt"> </span></font></pre><pre><font size="2" face="Courier New"><span style="font-size:10.0pt"> </span></font></pre>
<pre><font size="2" face="Courier New"><span style="font-size:10.0pt">On 2 Feb 2011, at 15:02, Oliver, Gavin wrote:</span></font></pre><pre><font size="2" face="Courier New"><span style="font-size:10.0pt"> </span></font></pre>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt" type="cite"><pre><font size="2" face="Courier New"><span style="font-size:10.0pt">Hi,</span></font></pre><pre><font size="2" face="Courier New"><span style="font-size:10.0pt"> </span></font></pre>
<pre><font size="2" face="Courier New"><span style="font-size:10.0pt">When I pull transcript variation alleles via the API, does the allele</span></font></pre></blockquote>
<pre><font size="2" face="Courier New"><span style="font-size:10.0pt">shown (e.g. A/T) represent the genomic base change, or the</span></font></pre><pre><font size="2" face="Courier New"><span style="font-size:10.0pt">transcriptomic one?</span></font></pre>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt" type="cite"><pre><font size="2" face="Courier New"><span style="font-size:10.0pt"> </span></font></pre><pre><font size="2" face="Courier New"><span style="font-size:10.0pt">Gavin</span></font></pre>
<pre><font size="2" face="Courier New"><span style="font-size:10.0pt"> </span></font></pre><pre><font size="2" face="Courier New"><span style="font-size:10.0pt"> </span></font></pre><pre><font size="2" face="Courier New"><span style="font-size:10.0pt">The contents of this message and any attachments to it are</span></font></pre>
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<pre><font size="2" face="Courier New"><span style="font-size:10.0pt">advise the sender.</span></font></pre>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt" type="cite"><pre><font size="2" face="Courier New"><span style="font-size:10.0pt"> </span></font></pre><pre><font size="2" face="Courier New"><span style="font-size:10.0pt">Almac Group (UK) Limited, registered no. NI061368. Almac Sciences</span></font></pre>
</blockquote>
<pre><font size="2" face="Courier New"><span style="font-size:10.0pt">Limited, registered no. NI041550. Almac Discovery Limited, registered</span></font></pre><pre><font size="2" face="Courier New"><span style="font-size:10.0pt">no. NI046249. Almac Pharma Services Limited, registered no. NI045055.</span></font></pre>
<pre><font size="2" face="Courier New"><span style="font-size:10.0pt">Almac Clinical Services Limited, registered no. NI041905. Almac</span></font></pre><pre><font size="2" face="Courier New"><span style="font-size:10.0pt">Clinical Technologies Limited, registered no. NI061202. Almac</span></font></pre>
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<pre><font size="2" face="Courier New"><span style="font-size:10.0pt">Almac House, 20 Seagoe Industrial Estate, Craigavon, BT63 5QD, UK. </span></font></pre>
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<pre><font size="2" face="Courier New"><span style="font-size:10.0pt">SC154034.</span></font></pre>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt" type="cite"><pre><font size="2" face="Courier New"><span style="font-size:10.0pt"> </span></font></pre><pre><font size="2" face="Courier New"><span style="font-size:10.0pt">Almac Clinical Services LLC, Almac Clinical Technologies LLC, Almac</span></font></pre>
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<p class="MsoNormal"><span lang="EN-GB" style="color:black;font-family:'Times New Roman'">Almac Sciences (Scotland) Limited, registered in Scotland no. SC154034. </span></p>
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<p class="MsoNormal"><span lang="EN-GB" style="color:black;font-family:'Times New Roman'">Almac Clinical Services LLC, Almac Clinical Technologies LLC, Almac Diagnostics LLC, Almac Pharma Services LLC and Almac Sciences LLC are Delaware limited liability companies and Almac Group Incorporated is a Delaware Corporation. More information on the Almac Group can be found on the Almac website: <a href="http://www.almacgroup.com" target="_blank">www.almacgroup.com</a></span></p>
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