[ensembl-dev] VEP - semicolons in variation database breaking VCF format

[Sarah Hunt]

Hi Dave,

Thanks for reporting this. We will update these records for our next 
release.

Best wishes,

Sarah

On 20/08/2014 11:05, David Parry wrote:
> Hello,
>
> I stumbled across a variant after annotating a VCF with the VEP (v76, offline,
> human, GRCh37) that broke the VCF format for downstream annotations. On
> inspection it appears that the 'Existing_variation' feature for this variant
> contains a semicolon.
>
> The variant is:
>
> X       153287314       .       TG      T
>
> And the offending annotation is:
>
> RettBASE_c.*8503delC;
>
> Having a quick grep for semicolons in the variation cache files there only
> appears to be one other such problem variant (CBS_c.103G>A;129G>A). These were
> present both in GRCh37 and GRCh38. I thought that it might be worth bringing
> to your attention in case other users run into this problem.
>
> Cheers
>
> Dave
>
>
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