[ensembl-dev] COSMIC annotations missing

[Guillermo Marco Puche]

Hello Will,

Good to know. We'll look forward in next VEP releases.

Thank you.

Regards,
Guillermo.


On 16/09/16 17:58, Will McLaren wrote:
> Correct - this is an undesirable feature, in that the allele check is 
> useful for those sources where we do have the alleles (the COSMIC 
> limitations prevent us from storing the alleles).
>
> We will fix this in a future VEP version.
>
> Regards
>
> Will
>
> On 16 September 2016 at 16:41, Guillermo Marco Puche 
> <guillermo.marco at sistemasgenomicos.com 
> <mailto:guillermo.marco at sistemasgenomicos.com>> wrote:
>
>     Hello Will,
>
>     Indeed I've both --check_existing and --check_alleles enabled. If
>     I disable --check_alleles COSMIC ids pop up. So the only way of
>     getting COSMIC is disabling allele check?
>
>     Regards,
>     Guillermo.
>
>
>     On 16/09/16 17:16, Will McLaren wrote:
>>     Hi Guillermo,
>>
>>     I don't see this issue - see attached screenshot.
>>
>>     I've also tested with the local script version and it works OK
>>     for me. Of course I'm assuming you have --check_existing enabled
>>     if you're running the script?
>>
>>     Regards
>>
>>     Will McLaren
>>     Ensembl Variation
>>
>>
>>     On 16 September 2016 at 12:37, Guillermo Marco Puche
>>     <guillermo.marco at sistemasgenomicos.com
>>     <mailto:guillermo.marco at sistemasgenomicos.com>> wrote:
>>
>>         Dear devs,
>>
>>         I'm aware of the COSMIC licensing changes. I'm trying to
>>         annotate a huge VCF with latest vep (85). I'm not getting any
>>         COSMIC annotation at all. The following two VCF variants have
>>         COSMIC annotations but I'm getting none with vep:
>>
>>         chr1    69224   .       A       C
>>         chr1    69230   .       A       C
>>
>>         Has been COSMIC removed from Ensembl public annotations even
>>         if VCF headers shows COSMIC=77? I thought that the previous
>>         releases would stay in Ensembl.
>>
>>         Regards,
>>         Guillermo
>>
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