[ensembl-dev] COSMIC annotations missing
Guillermo Marco Puche
guillermo.marco at sistemasgenomicos.com
Fri Sep 16 16:41:16 BST 2016
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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