vep_region
Predict variant consequences for genomic regions using Variant Effect Predictor (VEP), returning transcript effects, protein changes, and regulatory impacts.
Instructions
Predict variant consequences for a genomic region using the Variant Effect Predictor (VEP). Returns detailed consequence predictions including transcript effects, protein changes, and regulatory impacts.
Input Schema
TableJSON Schema
| Name | Required | Description | Default |
|---|---|---|---|
| species | No | Species name (e.g., human, mouse) | human |
| region | Yes | Genomic region in format chr:start-end:strand (e.g., 9:22125503-22125502:1) | |
| allele | Yes | Variant allele (e.g., C, T, DUP, DEL) | |
| canonical | No | Use only canonical transcripts | |
| ccds | No | Use CCDS transcripts | |
| gencode_basic | No | Use GENCODE basic transcripts | |
| mane | No | Use MANE (Matched Annotation from NCBI and EBI) transcripts | |
| refseq | No | Use RefSeq transcripts | |
| merged | No | Use merged Ensembl/RefSeq transcripts | |
| pick | No | Pick one consequence per variant | |
| pick_allele | No | Pick one consequence per variant allele | |
| pick_allele_gene | No | Pick one consequence per variant allele and gene | |
| per_gene | No | Use per-gene output | |
| hgvs | No | Include HGVS nomenclature | |
| protein | No | Include protein sequence | |
| domains | No | Include protein domains | |
| uniprot | No | Include UniProt identifiers | |
| tsl | No | Include transcript support level | |
| appris | No | Include APPRIS annotation | |
| numbers | No | Include affected exon/intron numbers | |
| variant_class | No | Include Sequence Ontology variant class | |
| AlphaMissense | No | Include AlphaMissense pathogenicity predictions | |
| CADD | No | Include CADD pathogenicity scores | |
| REVEL | No | Include REVEL pathogenicity scores | |
| Conservation | No | Include conservation scores | |
| LoF | No | Include Loss of Function predictions | |
| SpliceAI | No | Include SpliceAI splice-altering predictions | |
| distance | No | Distance to transcript (bp) for upstream/downstream variants | |
| minimal | No | Return minimal output | |
| shift_3prime | No | Shift variants to 3' end if possible | |
| transcript_version | No | Include transcript version numbers |