[ensembl-dev] VEP Custom annotation using BED

Genomeo Dev genomeodev at gmail.com
Tue Jun 10 18:22:46 BST 2014


Hi,

I would like to annotate a list of variants in VCF format with a BED file
using VEP script with 'overlap' annotation type. For this VEP requires
bed.gz and bed.gz.tabi:

http://www.ensembl.org/info/docs/tools/vep/script/vep_custom.html

Given that coordinates in VCF are 1-based and in BED are 0-based, I would
like to confirm that VEP takes that into account. Also, is tabix -0 option
not required in generating the index file (as indicated in the above link)?

Thanks.

-- 
G.
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