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<p>Hi Will,<br>
</p>
<p><br>
</p>
<p>Thanks for your response.<br>
</p>
<p><br>
</p>
<p>I ran the VEP separately to produce an updated vcf and then tried the Gemini load.<br>
</p>
<p><br>
</p>
<p>The following is the content of the .sh wrapper I used:<br>
</p>
<p><br>
</p>
<div>
<div>#!/bin/sh</div>
<div>export DATADIR=/home/hicadmin/data/cpgenome</div>
<div>export BINDIR=/home/hicadmin/src/ensembl-tools/scripts/variant_effect_predictor</div>
<div>perl ${BINDIR}/variant_effect_predictor.pl -i ${DATADIR}/$1.vcf \<br>
</div>
<div> --cache \</div>
<div> --sift b \</div>
<div> --polyphen b \</div>
<div> --symbol \</div>
<div> --numbers \</div>
<div> --total_length \</div>
<div> -o ${DATADIR}/$1_vep.vcf \</div>
<div> --vcf \</div>
<div> --fields Consequence,Codons,Amino_acids,Gene,SYMBOL,Feature,EXON,PolyPhen,SIFT,Protein_position</div>
<div><br>
And the requested CSQ info line:<br>
</div>
<div><br>
</div>
<div>##INFO=<ID=CSQ,Number=.,Type=String,Description="Consequence type as predicted by VEP. Format: Consequence|Codons|Amino_acids|Gene|SYMBOL|Feature|EXON|PolyPhen|SIFT|Protein_position"><br>
</div>
<div><br>
</div>
<div>Looking at original vcf file that string is present, so that's where it originates, so I think I have run VEP against an already-annotated file, meaning I need to learn more and investigate more before posting again!<br>
</div>
<div><br>
</div>
<div>The original file had this:<br>
</div>
<div><br>
</div>
<div>
<div>##INFO=<ID=CSQ,Number=A,Type=String,Description="Consequence type as predicted by VEP. Format: Allele|Gene|Feature|Feature_type|Consequence|cDNA_position|CDS_position|Protein_position|Amino_acids|Codons|Existing_variation|EXON|INTRON|HGNC|MOTIF_NAME|MOTIF_POS|HIGH_INF_POS|MOTIF_SCORE_CHANGE|DISTANCE|CANONICAL|SIFT|PolyPhen|GMAF|ENSP|DOMAINS|CCDS|HGVSc|HGVSp|CELL_TYPE"><br>
</div>
</div>
<div><br>
</div>
<div>Thanks,<br>
</div>
<div>Phil<br>
</div>
<div><br>
</div>
<div><span style="font-family: Calibri, sans-serif; font-size: 10pt;">Phil Appleby</span><br>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" color="#000000" style="font-size:11pt"><b>From:</b> dev-bounces@ensembl.org <dev-bounces@ensembl.org> on behalf of Will McLaren <wm2@ebi.ac.uk><br>
<b>Sent:</b> 03 April 2014 10:44<br>
<b>To:</b> Ensembl developers list<br>
<b>Subject:</b> Re: [ensembl-dev] Possible problems using the Variant Effect Predictor</font>
<div> </div>
</div>
<div>
<div dir="ltr">Hi Phil,<br>
<br>
<div>I don't believe that the string " infant death syndrome, association " is being added to the output by the VEP - there aren't any options in the core VEP code that could add such a string to the output.
<div><br>
</div>
<div>I don't know exactly what Gemini does but it may be that it is adding phenotype-based information somehow, possibly using a VEP plugin?</div>
<div><br>
</div>
<div>Could you send me the header line from your results file that contains the CSQ INFO description? It will look something like:</div>
<div><br>
</div>
<div>##INFO=<ID=CSQ,Number=.,Type=String,Description="Consequence type as predicted by VEP. Format: Allele|Gene|Feature|Feature_type|Consequence|cDNA_position|CDS_position|Protein_position|Amino_acids|Codons|Existing_variation|DISTANCE|STRAND"></div>
<div><br>
</div>
<div>I'd suggest contacting the Gemini developers also if you haven't already.</div>
<div><br>
</div>
<div>Regards</div>
<div><br>
</div>
<div>Will McLaren</div>
<div>Ensembl Variation<br>
<div class="gmail_extra"><br>
<br>
<div class="gmail_quote">On 3 April 2014 10:32, Philip Appleby <span dir="ltr"><<a href="mailto:p.appleby@dundee.ac.uk" target="_blank">p.appleby@dundee.ac.uk</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex; border-left-width:1px; border-left-color:rgb(204,204,204); border-left-style:solid; padding-left:1ex">
<div dir="ltr">
<div style="font-size:12pt; font-family:Calibri,Arial,Helvetica,sans-serif">
<div style="color:rgb(40,40,40); font-size:15px; font-family:'Segoe UI WPC','Segoe UI',Tahoma,'Microsoft Sans Serif',Verdana,sans-serif">
<font face="Calibri,Arial,Helvetica,sans-serif" size="3" color="black"><span style="font-size:12pt">
<div><font face="Calibri,Arial,Helvetica,sans-serif">
<div><font face="Calibri,Arial,Helvetica,sans-serif">
<div style="margin-top:0px; margin-bottom:0px">Hi,<br>
</div>
<div style="margin-top:0px; margin-bottom:0px"><br>
</div>
<div style="margin-top:0px; margin-bottom:0px">This question relates to problems found in while using the script '<a href="http://variant_effect_predictor.pl" target="_blank">variant_effect_predictor.pl</a>', version 75.<br>
</div>
<div style="margin-top:0px; margin-bottom:0px"><br>
</div>
<div style="margin-top:0px; margin-bottom:0px">I have been experimenting with annotating a VCF file (output from a personal genome sequencing run on an Illumina HiSeq 2000 machine) for loading into Gemini (<a href="http://gemini.readthedocs.org/en/latest/index.html" target="_blank">http://gemini.readthedocs.org/en/latest/index.html</a>) using
VEP as recommended in the Gemini documentation.<br>
</div>
<div style="margin-top:0px; margin-bottom:0px"><br>
</div>
<div style="margin-top:0px; margin-bottom:0px">I find that the Gemini parse and load fails with an error seemingly due to tabs embedded in one of the annotation strings (where the string " <font face="Segoe UI,Helvetica,Arial,sans-serif">infant death
syndrome, association </font>" appears meaning that the simple split('\t') statement in the parser is fooled.<br>
</div>
<div style="margin-top:0px; margin-bottom:0px"><br>
</div>
<div style="margin-top:0px; margin-bottom:0px">I have reproduced one of the offending lines below, my apologies for not knowing more about VEP, it's my first time using I don't understand the vertical bar delimited text yet.<br>
</div>
<div>
<div style="margin-top:0px; margin-bottom:0px"><br>
</div>
<div><font face="Tahoma" size="1"><span style="font-size:13px">
<div style="margin:0px"><font face="Segoe UI,Helvetica,Arial,sans-serif" size="3"><span style="font-size:12pt">
<div>chr18 907710 rs2856966 A G 108 PASS VARTYPE_SNV;hgmd_alleles=A/G;hgmd_id=CM092913;hgmd_disease=Sudden;CSQ=upstream_gene_variant|||ENSG00000265179|RP11-672L10.2|ENST00000582921||||,missense_variant|gAt/gGt|D/G|ENSG00000141433|ADCYAP1|ENST00000579794|2/4|benign(0.001)|tolerated(0.33)|54/176,missense_variant|gAt/gGt|D/G|ENSG00000141433|ADCYAP1|ENST00000450565|3/5|benign(0.001)|tolerated(0.33)|54/176,upstream_gene_variant|||ENSG00000265179|RP11-672L10.2|ENST00000580612||||,upstream_gene_variant|||ENSG00000265179|RP11-672L10.2|ENST00000577358||||,upstream_gene_variant|||ENSG00000265179|RP11-672L10.2|ENST00000581719||||,upstream_gene_variant|||ENSG00000265671|RP11-672L10.3|ENST00000582554||||,non_coding_exon_variant&nc_transcript_variant|||ENSG00000141433|ADCYAP1|ENST00000269200|1/3|||,upstream_gene_variant|||ENSG00000141433|ADCYAP1|ENST00000581602||||
infant death syndrome, association with;hgmd_gene=ADCYAP1;AA=A;EUR_AF=G:0.22;AMR_AF=G:0.17;AF=G:0.15;AFR_AF=G:0.11;ASN_AF=G:0.06;CSQ=G||NM_001099733.1|Transcript|missense_variant|280|161|54|D/G|gAt/gGt||3/5||ADCYAP1||||||YES|tolerated(0.6)|benign(0.001)|G:0.147|NP_001093203.1|||NM_001099733.1:c.161A>G|NP_001093203.1:p.Asp54Gly|,G||NM_001117.3|Transcript|missense_variant|252|161|54|D/G|gAt/gGt||2/4||ADCYAP1|||||||tolerated(0.6)|benign(0.001)|G:0.147|NP_001108.2|||NM_001117.3:c.161A>G|NP_001108.2:p.Asp54Gly|
GT:GQX:DPU:DPF:AU 0/1:108:25:2:11,0,10,0</div>
<div><br>
</div>
</span></font></div>
<div style="margin:0px"><font size="3"><span style="font-size:12pt"><font face="Calibri,Arial,Helvetica,sans-serif">I was wondering if you'd seen this kind of problem before.</font><br>
</span></font></div>
<div style="margin:0px"><font size="3"><span style="font-size:12pt"><br>
</span></font></div>
<div style="margin:0px"><font face="Segoe UI,Helvetica,Arial,sans-serif" size="3"><span style="font-size:12pt"><font face="Calibri,Arial,Helvetica,sans-serif">Thanks</font><br>
</span></font></div>
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