[ensembl-dev] ensembl-variation: import_vcf OK, but linking variations to transcripts ?

[Jan Vogel]

Hello, 

I have imported a VCF-file into a ensembl-variation database which I created from scratch - but i failed to link the variations / alleles / variation features to transcript_variations. 

The documentation on the import_vcf.pl script can be found here: 

 http://uswest.ensembl.org/info/docs/variation/import_vcf.html#transcript_variation

In the documentation ("transcript_variation" section) it says: 

"It may also be faster to do this once the VCF import is finished using the standard transcript_variation pipeline." 

Can someone point me to some documentation on the standard transcript-variation pipeline and how to run it?

I've tried to use the parallel_transcript_variation.pl script but it seems that this is working with some old schema (v58?). 

Any hint or draft of some documentation / command history is welcome. Also, is there a way to limit the linking of variations to genes /transcripts to specific logic-names ? I have various gene-sets in my core db and like to limit the consequence / transcript variation to only the canonical transcripts of one gene set. 
 

Thanks, 

   Jan