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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Hi Anja,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">This is the command from the web:<o:p></o:p></span></p>
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<span style="font-size:9.5pt;font-family:"Courier New";color:#666666">./vep --af --appris --biotype --buffer_size 500 --check_existing --distance 5000 --mane --polyphen b --pubmed --regulatory --sift b --species homo_sapiens --symbol --transcript_version --tsl
--uniprot --cache --input_file [input_data] --output_file [output_file]<o:p></o:p></span></p>
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<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">Attached is a vcf file.<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">Thanks,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Dayana<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>
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<p class="MsoNormal"><b><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">From:</span></b><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> Dev <dev-bounces@ensembl.org>
<b>On Behalf Of </b>Anja Thormann<br>
<b>Sent:</b> Monday, 28 October 2019 11:01<br>
<b>To:</b> Ensembl developers list <dev@ensembl.org><br>
<b>Subject:</b> Re: [ensembl-dev] output I get for my input file different when I use the web VEP and command line VEP<o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Dear Dayana,<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">could you please share which options you are using for the web tool? You can copy the command line equivalent from the job details section. Could you also please share an example for which you are seeing different annotations?<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Thank you,<o:p></o:p></p>
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<p class="MsoNormal">Anja<o:p></o:p></p>
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<o:p></o:p></p>
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<p class="MsoNormal">On 28 Oct 2019, at 07:06, Dayana Yahalomi <<a href="mailto:dayana.yahalomi@weizmann.ac.il">dayana.yahalomi@weizmann.ac.il</a>> wrote:<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">Dear Ensembl dev,<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">I have installed the following vep program<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">Versions:<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> ensembl : 98.e98e194<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> ensembl-funcgen : 98.36eef94<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> ensembl-io : 98.052d23b<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> ensembl-variation : 98.7b96c96<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> ensembl-vep : 98.2<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">And When I run the following command (offline):<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">./vep --verbose --species homo_sapiens --assembly GRCh38 --offline --dir_cache=/bio/db/vep98 --input_file ex2.vcf --format vcf --output_file outputfile_uniprot.vep98.2_dayana2.vcf
--vcf --uniprot<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">I don’t get the same results as running the same file example in your web.<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">I am interested in the protein changes and I look at the SwissProt flag. I used the protein name from SWISSPROT flag and go to the position indicated (Protein_position) and
look if it is correct.<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">In this case I get fewer protein changes and 30% are incorrect comparing to the web outfile where I get twice as much protein changes and only 10% are incorrect (this is probably
due to different isoforms than the one in Swissprot).<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">Do you know why I see these differences in the vcf outfile?<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">Thanks in advance,<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">Dayana<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:9.0pt;font-family:"Helvetica",sans-serif">_______________________________________________<br>
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