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

[Will McLaren]

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 -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> 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> 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>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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