<div dir="ltr">Hi Duarte,<div><br></div><div>Are you sure you have everything (cache, API, script) up to date?</div><div><br></div><div>It works fine for me using --symbol</div><div><br></div><div>Try the following input:</div>
<div><br></div><div>11 3762252 3762252 C/T 1<br></div><div><br></div><div>This is my output:</div><div><br></div><div>> perl <a href="http://variant_effect_predictor.pl">variant_effect_predictor.pl</a> -offline -i mouse_test.txt -force -symbol -species mus_musculus -dir /data/blastdb/Ensembl/vep/ -o stdout</div>
<div><div>## ENSEMBL VARIANT EFFECT PREDICTOR v73</div><div>## Output produced at 2013-11-06 11:12:41</div><div>## Connected to </div><div>## Using cache in /data/blastdb/Ensembl/vep//mus_musculus/73</div><div>## Using API version 73, DB version ?</div>
<div>## Extra column keys:</div><div>## DISTANCE : Shortest distance from variant to transcript</div><div>## SYMBOL : Gene symbol (e.g. HGNC)</div><div>#Uploaded_variation Location Allele Gene Feature Feature_type Consequence cDNA_position CDS_position Protein_position Amino_acids Codons Existing_variation Extra</div>
<div>rs26884575 11:3762252 T ENSMUSG00000020435 ENSMUST00000135250 Transcript intron_variant,nc_transcript_variant - - - - - - SYMBOL=Osbp2</div><div>rs26884575 11:3762252 T ENSMUSG00000020435 ENSMUST00000070552 Transcript intron_variant</div>
<div> - - - - - - SYMBOL=Osbp2</div><div>rs26884575 11:3762252 T ENSMUSG00000020435 ENSMUST00000127371 Transcript intron_variant</div><div> - - - - - - SYMBOL=Osbp2</div>
<div>rs26884575 11:3762252 T ENSMUSG00000020435 ENSMUST00000155197 Transcript intron_variant</div><div> - - - - - - SYMBOL=Osbp2</div></div><div><br></div>
<div>Cheers</div><div><br></div><div>Will</div><div><br></div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On 6 November 2013 11:00, Duarte Molha <span dir="ltr"><<a href="mailto:Duarte.Molha@ogt.com" target="_blank">Duarte.Molha@ogt.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-GB" link="blue" vlink="purple"><div><p class="MsoNormal">Dear Developers<u></u><u></u></p><p class="MsoNormal">
<u></u> <u></u></p><p class="MsoNormal">I am running an annotation of a mouse sample and would like to output the gene name in addition to the ensembl gene identifier…<u></u><u></u></p><p class="MsoNormal">Is there a way to do this on the script? I used the symbol field but that in not outputting anything <u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p><p class="MsoNormal">(I’m on v73)<u></u><u></u></p><p class="MsoNormal"><u></u> <u></u></p><p class="MsoNormal">Thanks<span class="HOEnZb"><font color="#888888"><u></u><u></u></font></span></p>
<span class="HOEnZb"><font color="#888888"><p class="MsoNormal"><u></u> <u></u></p><p class="MsoNormal"><span style="font-size:9.0pt;font-family:"Arial","sans-serif"">Duarte Molha</span><span> <u></u><u></u></span></p>
<p class="MsoNormal"><u></u> <u></u></p></font></span></div></div><br>_______________________________________________<br>
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