<div> </div>
<div>Thanks Stuart - that's really useful.</div>
<div> </div>
<div>Slashes are the required allele delimiter - the input with a comma is being treated as biallelelic, with the alt allele as "-,A" which the HGVS jiggerypokkery code refuses to deal with at all.</div>
<div> </div>
<div>The variant coordinates aren't logically compatible with the allele options which is why it's complaining - G/A looks like a substitution, but the coordinates look like a frameshift. We can probably make it handle this sort of thing a little more gracefully, but I wouldn't trust such inputs.</div>
<div><br> </div>
<div>Looking at the dbSNP record:</div>
<div> </div>
<div><a href="http://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?rs=rs55927445" target="_blank">http://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?rs=rs55927445</a></div>
<div> </div>
<div>it looks as if 2 neighbouring indels have been merged, suggesting this may not be the most reliable of variants.</div>
<div> </div>
<div> </div>
<div>Sarah </div>
<div><br> </div>
<div class="gmail_quote">On Wed, May 8, 2013 at 2:57 PM, Stuart Meacham <span dir="ltr"><<a href="mailto:sm766@cam.ac.uk" target="_blank">sm766@cam.ac.uk</a>></span> wrote:<br>
<blockquote style="BORDER-LEFT:#ccc 1px solid;MARGIN:0px 0px 0px 0.8ex;PADDING-LEFT:1ex" class="gmail_quote">Hi<br><br>Thanks for the reply, it seems that my source alternate allele(s) had slashes ('/') instead of commas (',') which were ok for the VEP but not for the TranscriptVariationAllele.pm when doing it's HGVS jiggerypokkery!<br>
<br>eg:<br><br>X 2726228 2726230 G/-,A + rs55927445<br><br>is fine<br><br>X 2726228 2726230 G/-/A + rs55927445<br><br>is not<br><br>even though this is how it is displayed in ensembl @ <a href="http://www.ensembl.org/Homo_sapiens/Variation/Summary?r=X:2725728-2726728;source=dbSNP;v=rs55927445;vdb=variation;vf=12794020" target="_blank">http://www.ensembl.org/Homo_<u></u>sapiens/Variation/Summary?r=X:<u></u>2725728-2726728;source=dbSNP;<u></u>v=rs55927445;vdb=variation;vf=<u></u>12794020</a><br>
<br>Thanks<br><br>Stuart
<div><br><br>On 08/05/13 13:09, Sarah Hunt wrote:<br></div>
<blockquote style="BORDER-LEFT:#ccc 1px solid;MARGIN:0px 0px 0px 0.8ex;PADDING-LEFT:1ex" class="gmail_quote">
<div>Hi Stuart,<br>Hope all goes well with you! Do you have any input you can share to help debug this one?<br>Sarah<br><br></div>
<div>
<div>On Wed, May 8, 2013 at 12:02 PM, Stuart Meacham <<a href="mailto:sm766@cam.ac.uk" target="_blank">sm766@cam.ac.uk</a> <mailto:<a href="mailto:sm766@cam.ac.uk" target="_blank">sm766@cam.ac.uk</a>>> wrote:<br>
<br> Hi,<br><br> When using the VEP (Ensembl 71) with apparently well formed data I<br> am getting some errors generated by the above mentioned module. It<br> appears $hgvs_notation->{type} is queried when not defined at<br>
several locations in the module. I am using the 'ensembl' data<br> format as input and outputting a vcf with the --everything flag.<br> The VEP is producing output for all 715 records provided. The<br> errors are for locations on ch1 and chrX.<br>
<br> For reference:<br><br> Use of uninitialized value in string eq at<br> /home/sm766/src/vep/variant_<u></u>effect_predictor/Bio/EnsEMBL/<u></u>Variation/<u></u>TranscriptVariationAllele.pm<br> line 934.<br>
Use of uninitialized value in string eq at<br> /home/sm766/src/vep/variant_<u></u>effect_predictor/Bio/EnsEMBL/<u></u>Variation/<u></u>TranscriptVariationAllele.pm<br> line 938.<br> Use of uninitialized value in string eq at<br>
/home/sm766/src/vep/variant_<u></u>effect_predictor/Bio/EnsEMBL/<u></u>Variation/<u></u>TranscriptVariationAllele.pm<br> line 976.<br> Use of uninitialized value in string eq at<br> /home/sm766/src/vep/variant_<u></u>effect_predictor/Bio/EnsEMBL/<u></u>Variation/<u></u>TranscriptVariationAllele.pm<br>
line 984.<br> Use of uninitialized value in string eq at<br> /home/sm766/src/vep/variant_<u></u>effect_predictor/Bio/EnsEMBL/<u></u>Variation/<u></u>TranscriptVariationAllele.pm<br> line 753.<br> Use of uninitialized value in string eq at<br>
/home/sm766/src/vep/variant_<u></u>effect_predictor/Bio/EnsEMBL/<u></u>Variation/<u></u>TranscriptVariationAllele.pm<br> line 769.<br> Use of uninitialized value in string eq at<br> /home/sm766/src/vep/variant_<u></u>effect_predictor/Bio/EnsEMBL/<u></u>Variation/<u></u>TranscriptVariationAllele.pm<br>
line 775.<br> Use of uninitialized value in string eq at<br> /home/sm766/src/vep/variant_<u></u>effect_predictor/Bio/EnsEMBL/<u></u>Variation/<u></u>TranscriptVariationAllele.pm<br> line 775.<br> Use of uninitialized value in string eq at<br>
/home/sm766/src/vep/variant_<u></u>effect_predictor/Bio/EnsEMBL/<u></u>Variation/<u></u>TranscriptVariationAllele.pm<br> line 806.<br> Use of uninitialized value in string eq at<br> /home/sm766/src/vep/variant_<u></u>effect_predictor/Bio/EnsEMBL/<u></u>Variation/<u></u>TranscriptVariationAllele.pm<br>
line 825.<br><br> Thanks<br><br> Stuart<br><br><br> ______________________________<u></u>_________________<br></div></div> Dev mailing list <a href="mailto:Dev@ensembl.org" target="_blank">Dev@ensembl.org</a> <mailto:<a href="mailto:Dev@ensembl.org" target="_blank">Dev@ensembl.org</a>>
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