[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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