[ensembl-dev] Variant Effect Predictor and VCF output

[Will McLaren]

Hi Fedor,

Currently there is no standard way to describe consequences in VCF;
the main issue to overcome is that our output format provides one line
per variant/allele/transcript, whereas VCF mandates one line per
variant. This means we'd have to squeeze an awful lot of information
into the INFO column of the VCF.

We should, however, be able to provide at least summary level
information in the INFO field, and this is what we will look into
doing, as we have had several requests for VCF output to be a feature
of the VEP.

I am not aware of any tools to convert, however, I think a simple perl
script and using the --most_severe or --summary options (both of which
output only one line per variant) in the VEP you should be able to
combine the original VCF with the output.

Hope this helps

Will McLaren
Ensembl Variation

On 9 November 2011 20:03, Fedor Gusev <gusevfe at gmail.com> wrote:
> Hello everyone.
>
> How come it is not possible for VEP to output a vcf file? Are there
> any tools to convert the output to VCF?
>
> --
> Kind regards,
> Fedor Gusev.
>
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