[ensembl-dev] variant effect predictor 2.0 question

[Graham Ritchie]

Hi Mark,

If you could give us a (preferably small) example input file where you get significantly different results between versions that will help us investigate this.

Thanks,

Graham

Ensembl variation


On 14 Jul 2011, at 14:14, Mark Aquino wrote:

> Hi, 
> 
> 	I've been trying to switch over to the new version of the VEP (2.x) but have been getting some strange output.  Basically, it seems like the normal output is multiplied by 4 or 5 times (or more).  For one run on an output that was 70K lines using the original variant effect predictor I got over 1 million lines of output consisting of the each transcript being analyzed and/or output 10+ times each, and on a subsequent re-run I got 330K lines of output with each being repeated 5 times.  (I checked this by doing a simple grep on the output with line numbers to ensure that there weren't just more transcripts per variation being repeated).  
> 
> Has anyone else experienced this issue?
> 
> 
> Best,
> Mark Aquino
> 
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