[ensembl-dev] VEP - feature request - VCF output file as an additional output file

[Will McLaren]

Hi Duarte,

Thanks for the suggestion - I'll consider it for the next version of the VEP.

In the meantime, I think it would be fairly easy to write a script to
convert from the VCF output to the regular tab-delimited output, if
you were so inclined. The VCF contains all the data that you would
require to reconstitute the tab-delimited output.

Cheers

Will

On 10 May 2012 17:27, Duarte Molha <Duarte.Molha at ogt.co.uk> wrote:
> I am having fun with the latest VEP. Thank you for the hard work!
>
>
>
> However I would like to make a feature request... Could you make the  –VCF
> behaviour different?
>
>
>
> It would be great if the script could output the annotation in regular tab
> delimited format and the –VCF flag could be used to specify a additional
> output filename for the same data in VCF format.
>
>
>
> The VCF format is very useful and portable but for some things but it would
> be a headache to parse the variant annotations from the info field so it
> would be great it from 1 run we could get both files.
>
>
>
> Cheers,
>
> Duarte Molha
>
>
>
>
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