[ensembl-dev] FW: downstream.pm VEP plugin

[Sarah Hunt]

Dear Manuel,

This plugin uses data structures created by VEP to provide additional 
information, so it would not be trivial to adapt it to annotate input 
from a different program.

Assuming you are using ensembl transcripts, there is an example in the 
variation tutorial:

http://www.ensembl.org/info/docs/api/variation/variation_tutorial.html

which may help you in creating the VariationFeature and 
TranscriptVariations objects required by the plugin from a novel input.

Best wishes,

Sarah

On 07/07/2014 12:37, Manuel Tardáguila Sancho wrote:
> To whom it may concern,
>
> My name is Manuel Tardaguila and I am an MSC in bioinformatics doing a 
> project in the university of Lausanne. I am working on annotated 
> variations using VEP and snpEff as annotators.
>
> For frameshift variants I have to calculate downstream effects and I 
> have found this plugin made by your team. I have a question that I 
> would be very grateful if you could address;
>
> As happens with other VEP plugins, I suppose that downstream plugin is 
> called from VEP command line when the program is run. In case I have 
> an annotated output from a different program (i.e. snpEff) would it be 
> possible to adapt the plugin or run it separately of VEP?
>
> Thanks in advance for your time and patience,
>
> ------------------------------------------------------------------------
> From: manueltar at hotmail.com
> To: dev at ensembl.org
> Subject: downstream.pm VEP plugin
> Date: Mon, 7 Jul 2014 13:33:57 +0200
>
> Dear Mr Mclaren,
>
> My name is Manuel Tardaguila and I am an MSC in bioinformatics doing a 
> project in the university of Lausanne. I am working on annotated 
> variations using VEP and snpEff as annotators.
>
> For frameshift variants I have to calculate downstream effects and I 
> have found this plugin made by your team. I have a question that I 
> would be very grateful if you could address;
>
> As happens with other VEP plugins, I suppose that downstream plugin is 
> called from VEP command line when the program is run. In case I have 
> an annotated output from a different program (i.e. snpEff) would it be 
> possible to adapt the plugin or run it separately of VEP?
>
> Thanks in advance for your time and patience,
>
>
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