The Ensembl Variant Effect Predictor

Table 7 Example filters available in the VEP

Option or command	Description
Runtime filters
--no_intergenic	Filter out variants that fall in intergenic regions
--pick	Choose one consequence for each variant; priority is given to the canonical transcript for each gene, protein coding transcripts, and more severe consequence types e.g., missense_variant is more severe than intron_variant
--per_gene	Picks one consequence using the same methodology as --pick but chooses one per overlapping gene
--filter_common	Filter out variants that are co-located with a known variant that has a minor allele frequency greater than 1 %.
Results filters using filter_vep.pl
SIFT is deleterious OR PolyPhen is probably_damaging	Filter for results where SIFT or PolyPhen-2 predicts the variant protein will be non-functional
AFR >0.1 AND EUR <0.05	Filter for variants co-located with those that are common in African populations but rare in European populations
Gene in gene_list.txt AND Phenotype matches cancer	Filter for results for variants that fall in the genes with IDs listed in gene_list.txt and that have been annotated with a cancer phenotype from a custom dataset (VEP script only)