updated_docs_for_reg_gff - #985
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Aug 27, 2026
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| <pre class="code sh_sh">./vep -i input.vcf --cache --regulatory_gff file=regulatory_features.gff3.gz,motifs=motif_features.gff3.gz,emars=EMARs.gff.gz</pre> | ||
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| <p> <b>file=</b> is required; the rest are optional and independent. As with transcript <a href="#gff">GFF/GTF files</a>, each file must be sorted in chromosomal order, bgzipped and indexed with tabix. The files published by Ensembl are already bgzipped, so if no index is supplied alongside one, it is enough to create it: </p> |
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needs to change. not a requirement.
| epigenetically modified accessible region GFF3). | ||
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| Features from <b>file</b> and <b>emars</b> have a Feature type of | ||
| RegulatoryFeature and the consequence regulatory_region_variant, with |
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We may have other consequence too, like regulatory_region_amplification ?
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I won't make the list exhaustive I'll make it clear that this is an example for short variants.
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| <p> The feature type — <b>promoter</b>, <b>enhancer</b>, <b>CTCF_binding_site</b>, <b>open_chromatin_region</b> and so on — is reported under BIOTYPE. Every type yields the <b>regulatory_region_variant</b> consequence, with BIOTYPE distinguishing it, matching the behaviour of a cache or database regulatory source. Any feature type Ensembl VEP does not recognise is skipped with a warning. </p> | ||
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| <p> <b>emars=</b> reads a second regulatory-feature file (of type EMAR) as an additional source. EMARs are broad container regions that overlap many regulatory features, so enabling them typically adds a second annotation line to variants that already overlap a promoter, enhancer or CTCF binding site. Note that the funcgen database source excludes EMARs, so this is a deliberate addition rather than a match of database behaviour. </p> |
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| <p> <b>emars=</b> reads a second regulatory-feature file (of type EMAR) as an additional source. EMARs are broad container regions that overlap many regulatory features, so enabling them typically adds a second annotation line to variants that already overlap a promoter, enhancer or CTCF binding site. Note that the funcgen database source excludes EMARs, so this is a deliberate addition rather than a match of database behaviour. </p> | |
| <p> <b>emars=</b> reads a second regulatory-feature file (of type EMAR) as an additional source. EMARs are broad container regions that overlap many regulatory features, so enabling them typically adds a second annotation line to variants that already overlap a promoter, enhancer or CTCF binding site. Note that the funcgen database source excludes EMARs, so this is an additional feature in GFF and not available via database. </p> |
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| <h3 id="reg_gff_features">Regulatory features (file=, emars=)</h3> | ||
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| <p> The feature type — <b>promoter</b>, <b>enhancer</b>, <b>CTCF_binding_site</b>, <b>open_chromatin_region</b> and so on — is reported under BIOTYPE. Every type yields the <b>regulatory_region_variant</b> consequence, with BIOTYPE distinguishing it, matching the behaviour of a cache or database regulatory source. Any feature type Ensembl VEP does not recognise is skipped with a warning. </p> |
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same, other consequence type?
Co-authored-by: Syed Nakib Hossain <snhossain@ebi.ac.uk>
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Updating the docs in line with the PR to add regulatory CSQ calcs from GFF - see here for more details: Ensembl/ensembl-vep#2042
DO NOT MERGE UNTIL VEP PR IS IN