Runtime filters
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--no_intergenic
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Filter out variants that fall in intergenic regions
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--pick
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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
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--per_gene
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Picks one consequence using the same methodology as --pick but chooses one per overlapping gene
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--filter_common
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Filter out variants that are co-located with a known variant that has a minor allele frequency greater than 1 %.
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Results filters using filter_vep.pl
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SIFT is deleterious OR PolyPhen is probably_damaging
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Filter for results where SIFT or PolyPhen-2 predicts the variant protein will be non-functional
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AFR >0.1 AND EUR <0.05
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Filter for variants co-located with those that are common in African populations but rare in European populations
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Gene in gene_list.txt AND Phenotype matches cancer
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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)
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