[ensembl-dev] Possible problems using the Variant Effect Predictor

Thu Apr 3 10:44:34 BST 2014

Hi Phil,

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.

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?

Could you send me the header line from your results file that contains the
CSQ INFO description? It will look something like:

I'd suggest contacting the Gemini developers also if you haven't already.

Regards

Will McLaren
Ensembl Variation

On 3 April 2014 10:32, Philip Appleby <p.appleby at dundee.ac.uk> wrote:

>    Hi,
>  
>  This question relates to problems found in while using the script '
> variant_effect_predictor.pl', version 75.
>
>  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 (http://gemini.readthedocs.org/en/latest/index.html) using
> VEP as recommended in the Gemini documentation.
>
>  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 "    infant
>  death   syndrome,       association  " appears meaning that the simple
> split('\t') statement in the parser is fooled.
>
>  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.
>
>   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
>
>  I was wondering if you'd seen this kind of problem before.
>
>  Thanks
>  Phil
>
>  Phil Appleby
> Programmer
> Health Informatics Centre (HIC)
> University of Dundee
> Mackenzie Building
> Ninewells
> DD2 4BF
> +44 (0) 1382 383971
>
> The University of Dundee is a registered Scottish Charity, No: SC015096
>
>
>
>
>  Phil Appleby
>  Programmer
>  Health Informatics Centre (HIC)
>  University of Dundee
>  Mackenzie Building
>  Ninewells
>  DD2 4BF
>  +44 (0) 1382 383971
>
> The University of Dundee is a registered Scottish Charity, No: SC015096
>
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