Table 7 Example filters available in the VEP

 --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 %.

 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)