[ensembl-dev] Ref in output using VEP
Stuart Meacham
sm766 at cam.ac.uk
Tue May 14 09:51:16 BST 2013
Hi Will,
The former, and thanks!
Cheers
Stuart
On 14/05/2013 09:35, Will McLaren wrote:
> 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
> <mailto: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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