[ensembl-dev] Empty GMAF field in VEP (possible bug?)

[Guillermo Marco Puche]

Hello Will,

It must be my API then. Should I download it from Ensembl website or 
from a special repository with fix?

Regards,
Guillermo.

On 06/04/2013 01:25 PM, Will McLaren wrote:
> Have you updated your API?
>
> It works OK for me, here's a snippet of the output I get from:
>
> perl variant_effect_predictor.pl <http://variant_effect_predictor.pl> 
> -i maf.vcf -gmaf -cache -force
>
> #Uploaded_variation     Location        Allele  Gene  Feature 
> Feature_type    Consequence     cDNA_position CDS_position   
>  Protein_position        Amino_acids Codons  Existing_variation      Extra
> 17_41246532_T/- 17:41246532     -       ENSG00000012048 
> ENST00000352993 Transcript  intron_variant,feature_truncation       - 
>       -       -     -       -       rs80357618,rs80357911,CD951606 
>  CLIN_SIG=untested,untested
>
> Will
>
>
> On 4 June 2013 12:10, Guillermo Marco Puche 
> <guillermo.marco at sistemasgenomicos.com 
> <mailto:guillermo.marco at sistemasgenomicos.com>> wrote:
>
>     Hello Will,
>
>     Try with this input:
>
>     https://github.com/guillermomarco/vep_plugins_71/blob/master/wrong_gmaf/wrong.vcf
>
>     Regards,
>     Guillermo.
>
>
>     On 06/04/2013 10:05 AM, Will McLaren wrote:
>>     Hi Guillermo,
>>
>>     Can you provide some input that produces this problem?
>>
>>     It works OK for me...
>>
>>     Will
>>
>>
>>     On 3 June 2013 10:02, Guillermo Marco Puche
>>     <guillermo.marco at sistemasgenomicos.com
>>     <mailto:guillermo.marco at sistemasgenomicos.com>> wrote:
>>
>>         Hello Will,
>>
>>         Are you sure bug was fixed? I'm getting some ":,:" outputs.
>>         I'm using tab delimited format not VCF as output.
>>
>>         Regards,
>>         Guillermo.
>>
>>
>>         On 05/22/2013 12:44 PM, Duarte Molha wrote:
>>>
>>>         On Wed, May 22, 2013 at 11:42 AM, Duarte Molha
>>>         <duartemolha at gmail.com <mailto:duartemolha at gmail.com>> wrote:
>>>
>>>
>>>         Sorry will... replied essentially saying the same thing you
>>>         did... Should have refreshed my email client before sending :)
>>>
>>>         Thank you for the fix
>>>
>>>         =========================
>>>              Duarte Miguel Paulo Molha
>>>         http://about.me/duarte
>>>         =========================
>>>
>>>
>
>
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