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</o:shapelayout></xml><![endif]--></head><body lang=EN-GB link=blue vlink=purple><div class=WordSection1><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Hi Will<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>I just realised the issue. I had rearranged the field order and the fields option in VEP seems to be case sensitive.. I has calling in small caps and it does not display. When changed to SYMBOL it works flawlessly.<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Cheers,<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Duarte<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><b><span lang=EN-US style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>From:</span></b><span lang=EN-US style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'> dev-bounces@ensembl.org [mailto:dev-bounces@ensembl.org] <b>On Behalf Of </b>Will McLaren<br><b>Sent:</b> 06 November 2013 11:14<br><b>To:</b> Ensembl developers list<br><b>Subject:</b> Re: [ensembl-dev] Mouse Gene Symbols on VEP73<o:p></o:p></span></p><p class=MsoNormal><o:p> </o:p></p><div><p class=MsoNormal>Hi Duarte,<o:p></o:p></p><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>Are you sure you have everything (cache, API, script) up to date?<o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>It works fine for me using --symbol<o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>Try the following input:<o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>11 3762252 3762252 C/T 1<o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>This is my output:<o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>> 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<o:p></o:p></p></div><div><div><p class=MsoNormal>## ENSEMBL VARIANT EFFECT PREDICTOR v73<o:p></o:p></p></div><div><p class=MsoNormal>## Output produced at 2013-11-06 11:12:41<o:p></o:p></p></div><div><p class=MsoNormal>## Connected to <o:p></o:p></p></div><div><p class=MsoNormal>## Using cache in /data/blastdb/Ensembl/vep//mus_musculus/73<o:p></o:p></p></div><div><p class=MsoNormal>## Using API version 73, DB version ?<o:p></o:p></p></div><div><p class=MsoNormal>## Extra column keys:<o:p></o:p></p></div><div><p class=MsoNormal>## DISTANCE : Shortest distance from variant to transcript<o:p></o:p></p></div><div><p class=MsoNormal>## SYMBOL : Gene symbol (e.g. HGNC)<o:p></o:p></p></div><div><p class=MsoNormal>#Uploaded_variation Location Allele Gene Feature Feature_type Consequence cDNA_position CDS_position Protein_position Amino_acids Codons Existing_variation Extra<o:p></o:p></p></div><div><p class=MsoNormal>rs26884575 11:3762252 T ENSMUSG00000020435 ENSMUST00000135250 Transcript intron_variant,nc_transcript_variant - - - - - - SYMBOL=Osbp2<o:p></o:p></p></div><div><p class=MsoNormal>rs26884575 11:3762252 T ENSMUSG00000020435 ENSMUST00000070552 Transcript intron_variant<o:p></o:p></p></div><div><p class=MsoNormal> - - - - - - SYMBOL=Osbp2<o:p></o:p></p></div><div><p class=MsoNormal>rs26884575 11:3762252 T ENSMUSG00000020435 ENSMUST00000127371 Transcript intron_variant<o:p></o:p></p></div><div><p class=MsoNormal> - - - - - - SYMBOL=Osbp2<o:p></o:p></p></div><div><p class=MsoNormal>rs26884575 11:3762252 T ENSMUSG00000020435 ENSMUST00000155197 Transcript intron_variant<o:p></o:p></p></div><div><p class=MsoNormal> - - - - - - SYMBOL=Osbp2<o:p></o:p></p></div></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>Cheers<o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>Will<o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div></div><div><p class=MsoNormal style='margin-bottom:12.0pt'><o:p> </o:p></p><div><p class=MsoNormal>On 6 November 2013 11:00, Duarte Molha <<a href="mailto:Duarte.Molha@ogt.com" target="_blank">Duarte.Molha@ogt.com</a>> wrote:<o:p></o:p></p><div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>Dear Developers<o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> <o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>I am running an annotation of a mouse sample and would like to output the gene name in addition to the ensembl gene identifier…<o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>Is there a way to do this on the script? I used the symbol field but that in not outputting anything <o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> <o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>(I’m on v73)<o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> <o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>Thanks<o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='color:#888888'> <o:p></o:p></span></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='font-size:9.0pt;font-family:"Arial","sans-serif";color:#888888'>Duarte Molha</span><span style='color:#888888'> <o:p></o:p></span></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='color:#888888'> <o:p></o:p></span></p></div></div><p class=MsoNormal style='margin-bottom:12.0pt'><br>_______________________________________________<br>Dev mailing list <a href="mailto:Dev@ensembl.org">Dev@ensembl.org</a><br>Posting guidelines and subscribe/unsubscribe info: <a href="http://lists.ensembl.org/mailman/listinfo/dev" target="_blank">http://lists.ensembl.org/mailman/listinfo/dev</a><br>Ensembl Blog: <a href="http://www.ensembl.info/" target="_blank">http://www.ensembl.info/</a><o:p></o:p></p></div><p class=MsoNormal><o:p> </o:p></p></div></div></body></html>