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<p class="MsoNormal"><span style="color:#1F497D">Hello Sarah,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">I’m writing to confirm that the issue was solved, and also to report another very minor issue. I presume VEP is intended to output data in the same order as the records of the VCF input. This is almost entirely
the case for my data, but I find that a set of MT records gets inserted into the middle of the ChrY records near the end of the output. I’ve resorted the files to address this inconsistency, but I wanted to bring it to your attention. If I had to venture
a wild guess, perhaps this is due an error with multi-threading logic, in which the final records to return are flushed out of order?<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">Regards,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">Oliver<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"><o:p> </o:p></span></p>
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<p class="MsoNormal"><b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:windowtext">From:</span></b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:windowtext"> dev-bounces@ensembl.org [mailto:dev-bounces@ensembl.org]
<b>On Behalf Of </b>Sarah Hunt<br>
<b>Sent:</b> Thursday, February 05, 2015 4:22 AM<br>
<b>To:</b> Ensembl developers list<br>
<b>Subject:</b> Re: [ensembl-dev] VEP (ver78) TranscriptVariationAllele.pm unitialized value error with --hgvs enabled<o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal" style="margin-bottom:12.0pt"><br>
Hi Oliver,<br>
<br>
Thanks for the detailed report. This was a similar issue with a stop inserted before the stop not being handled well. It is fixed in branch78 so the consequence of the variant has changed from 'stop_gained' to 'stop_retained'. The HGVS string reflects the synonymous
status.<br>
<br>
Best wishes,<br>
<br>
Sarah<br>
<br>
<o:p></o:p></p>
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<p class="MsoNormal">On 03/02/2015 16:52, Homann, Oliver wrote:<o:p></o:p></p>
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<p class="MsoNormal"><span style="color:#1F497D">Apologies, forgot to clarify that the error occurs in line 1221 of the new version of TranscriptVariationAllele.pm:</span><o:p></o:p></p>
<p class="MsoNormal"><span style="color:#1F497D"> </span><o:p></o:p></p>
<p class="MsoNormal"><span style="color:#1F497D"> 1221 unless( $hgvs_notation->{ref} eq "-"){</span><o:p></o:p></p>
<p class="MsoNormal"><span style="color:#1F497D"> 1222 $hgvs_notation->{ref} = Bio::SeqUtils->seq3(Bio::PrimarySeq->new(-seq => $hgvs_notation->{ref}, -id => 'ref', -alphabet => 'protein')) || "";</span><o:p></o:p></p>
<p class="MsoNormal"><span style="color:#1F497D"> 1223 }</span><o:p></o:p></p>
<p class="MsoNormal"><span style="color:#1F497D"> </span><o:p></o:p></p>
<p class="MsoNormal"><span style="color:#1F497D">Regards,</span><o:p></o:p></p>
<p class="MsoNormal"><span style="color:#1F497D">Oliver</span><o:p></o:p></p>
<p class="MsoNormal"><span style="color:#1F497D"> </span><o:p></o:p></p>
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<p class="MsoNormal"><b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:windowtext">From:</span></b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:windowtext">
<a href="mailto:dev-bounces@ensembl.org">dev-bounces@ensembl.org</a> [<a href="mailto:dev-bounces@ensembl.org">mailto:dev-bounces@ensembl.org</a>]
<b>On Behalf Of </b>Homann, Oliver<br>
<b>Sent:</b> Tuesday, February 03, 2015 8:50 AM<br>
<b>To:</b> Ensembl developers list<br>
<b>Subject:</b> Re: [ensembl-dev] VEP (ver78) TranscriptVariationAllele.pm unitialized value error with --hgvs enabled</span><o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoNormal"><span style="color:#1F497D">Hello Sarah,</span><o:p></o:p></p>
<p class="MsoNormal"><span style="color:#1F497D"> </span><o:p></o:p></p>
<p class="MsoNormal"><span style="color:#1F497D">Your fix worked for all but one of my ‘uninitialized value’ errors. Would you mind trying to track down the issue with this remaining problematic entry?</span><o:p></o:p></p>
<p class="MsoNormal"><span style="color:#1F497D"> </span><o:p></o:p></p>
<p class="MsoNormal"><span style="color:#1F497D">#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SAMPLENAME</span><o:p></o:p></p>
<p class="MsoNormal"><span style="color:#1F497D">19 42355761 rs374945441 C CTAGAAA 885.10 . AC=1;AF=5.556e-03;AN=180;BaseQRankSum=-1.922e+00;DB;DP=2670;FS=2.561;GQ_MEAN=75.28;GQ_STDDEV=91.16;InbreedingCoeff=-0.0056;MLEAC=1;MLEAF=5.556e-03;MQ=60.00;MQ0=0;MQRankSum=-2.160e-01;NCC=0;QD=9.83;ReadPosRankSum=0.353;SOR=0.669
GT:AD:DP:GQ:PL 0/0:17,0:17:34:0,34,505</span><o:p></o:p></p>
<p class="MsoNormal"><span style="color:#1F497D"> </span><o:p></o:p></p>
<p class="MsoNormal"><span style="color:#1F497D">Thanks,</span><o:p></o:p></p>
<p class="MsoNormal"><span style="color:#1F497D">Oliver</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Times New Roman","serif""><br>
<br>
<br>
<o:p></o:p></span></p>
<pre>_______________________________________________<o:p></o:p></pre>
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<pre>Ensembl Blog: <a href="http://www.ensembl.info/">http://www.ensembl.info/</a><o:p></o:p></pre>
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<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Times New Roman","serif""><o:p> </o:p></span></p>
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