VEP behavior Problem

[jasonbhn]

VEP default use full GTF from ensembl. The consequence column takes into considerations of non protein coding transcript, therefore when only looking at high conf gene transcripts, "intron variants" shows up outside of gene, due to invisible exons.
Solution to this problem is to use SV location categories, ie when a variant is not genebody but VEP says intronic, change it to not intron variant.