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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) |
