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Table 7 Example filters available in the VEP

From: The Ensembl Variant Effect Predictor

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
 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)