<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">
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<div style="margin-top:0px;margin-bottom:0px">Hi,<br>
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<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>
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<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>
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<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>
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<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>
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<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>
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<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>
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<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>
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