[ensembl-dev] COSMIC annotations missing

[Guillermo Marco Puche]

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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