[ensembl-dev] variant effect predictor 2.0 question

Mark Aquino aquinom85 at me.com
Thu Jul 14 14:14:18 BST 2011


	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?

Mark Aquino

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