[ensembl-dev] Warning message on VEP script

Graham Ritchie grsr at ebi.ac.uk
Tue Nov 22 15:27:49 GMT 2011


Hi Duarte,

Thanks. OK, I see what's going on now. This variant falls in an incomplete stop codon, which is assigned an amino acid code of X, and the code that looks up sift and polyphen expects an unambiguous amino acid code. I will change the API to avoid warnings in these cases, but it shouldn't make any difference to your results as there won't be a sift or polyphen prediction for these cases. Hope that makes sense.

Cheers,

Graham


On 22 Nov 2011, at 15:02, Duarte Molha wrote:

> Dear Graham
> 
> Here is a vcf file with one variation that triggers the warning...
> 
> For reference here is the command I used:
> 
> variant_effect_predictor.pl -i sample.vcf  -o output.ann --protein --regulatory --sift=b --polyphen=b --condel=b --check_existing --verbose
> 
> Cheers
> 
>    Duarte
> 
> 
> -----Original Message-----
> From: Graham Ritchie [mailto:grsr at ebi.ac.uk] 
> Sent: 22 November 2011 14:14
> To: Duarte Molha
> Cc: Ensembl
> Subject: Re: [ensembl-dev] Warning message on VEP script
> 
> Hi Duarte,
> 
> This message means that somehow the script is looking for a sift or polyphen prediction in an unexpected position in a protein. I'm not sure why you're seeing this though, could you possibly send me an example input file that produces this error (preferably as small as possible) and I will look into it.
> 
> Cheers,
> 
> Graham
> 
> 
> On 22 Nov 2011, at 14:06, Duarte Molha wrote:
> 
>> Dear Devs.
>> 
>> I am sorry to be bothering you once more but I was wondering if any of you would be able to tell me what this waringin message might be referring to.
>> 
>> -------------------- WARNING ----------------------
>> MSG: Offset outside of prediction matrix for position 182 and amino acid R?
>> FILE: EnsEMBL/Variation/ProteinFunctionPredictionMatrix.pm LINE: 626
>> CALLED BY: EnsEMBL/Variation/ProteinFunctionPredictionMatrix.pm  LINE: 271
>> Ensembl API version = 64
>> ---------------------------------------------------
>> 
>> I get this when I run some of my VCF files though the script and I am not sure what to make of it.
>> 
>> Best regards
>> 
>> Duarte Molha
>> 
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> 
> <sample.vcf>





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