[ensembl-dev] Warning message on VEP script

[Graham Ritchie]

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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