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

[Will McLaren]

The main branch code for 71 contains the fix.

Will


On 4 June 2013 12:31, Guillermo Marco Puche <
guillermo.marco at sistemasgenomicos.com> wrote:

>  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 -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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>
>
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