[ensembl-dev] Ref in output using VEP

[Will McLaren]

Hi Stuart,

I'm not sure what you mean - do you want the reference allele in a column
on each row? Or do you want to consider the reference allele as an
alternate allele?

For the former, you'd have to write a plugin, something like:

package RefAllele;

use strict;
use warnings;

use base qw(Bio::EnsEMBL::Variation::Utils::BaseVepPlugin);

sub feature_types {
    return ['Feature','Intergenic'];
}

sub get_header_info {
    return {
        RefAllele => "Reference allele",
    };
}

sub run {
    my ($self, $tva) = @_;
    return { RefAllele => (split "/",
$tva->variation_feature->allele_string)[0] };
}

For the latter, I don't think it can be done, and wouldn't make much sense!

Regards

Will


On 14 May 2013 08:35, Stuart Meacham <sm766 at cam.ac.uk> wrote:

> Hi,
>
> Simple question: what is the easiest way to get the reference allele from
> a vcf formatted input file into a 'default' formatted output file whilst
> using the latest version of the Variant Effect Predictor?
>
> Thanks
>
> Stuart
>
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