[ensembl-dev] COSMIC annotations missing

[Will McLaren]

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> 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@
> 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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>
>
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