When calling variants it can be very useful to know what impact a polymorphism might have on the biology of an organism. It is often difficult to extend a simple list of variants to specific phenotypes, but it is possible to broadly classify a variant based on its possible impact on protein coding genes (e.g., mis-sense mutations, etc.). A very useful tool for performing such an analysis is the Varient Effect Predictor (VEP
) tool, which is produced by the folks at Ensembl. This tutorial will describe how to perform such an analysis on your organism of interest using variants stored in a VCF file and annotations from a GFF file.
VEP
must be installed. Detailed information on this tool and its installation can be found here.Boa_constrictor_SGA_7C_scaffolds.fa
: A genome FASTA file for your organism is requi