Opencravat Tools

Configuration File: opencravat_tools.json Tool Type: Local Tools Count: 2

This page contains all tools defined in the opencravat_tools.json configuration file.

Available Tools

OpenCRAVAT_annotate_variant (Type: OpenCRAVATTool)

Annotate a single genomic variant using OpenCRAVAT with 182+ annotation sources including ClinVar…

OpenCRAVAT_annotate_variant tool specification

Tool Information:

  • Name: OpenCRAVAT_annotate_variant

  • Type: OpenCRAVATTool

  • Description: Annotate a single genomic variant using OpenCRAVAT with 182+ annotation sources including ClinVar, gnomAD, SIFT, PolyPhen-2, REVEL, AlphaMissense, SpliceAI, GERP, PhastCons, DANN, FATHMM, and more. Returns gene name, amino acid change, consequence type, and all requested annotator results. Input: chromosome, position (1-based, GRCh38), reference and alternate alleles. Optionally specify which annotators to use (comma-separated).

Parameters:

  • chrom ([‘string’, ‘null’]) (optional) Chromosome (e.g., ‘chr17’, ‘chr7’, ‘17’). ‘chr’ prefix added automatically if missing.

  • chromosome ([‘string’, ‘null’]) (optional) Alias for chrom. Chromosome (e.g., ‘chr17’, ‘chr7’, ‘17’).

  • pos ([‘integer’, ‘null’]) (optional) Genomic position (1-based, GRCh38 coordinates)

  • position ([‘integer’, ‘null’]) (optional) Alias for pos. Genomic position (1-based, GRCh38 coordinates).

  • ref_base ([‘string’, ‘null’]) (optional) Reference allele (e.g., ‘C’, ‘A’, ‘G’, ‘T’)

  • ref ([‘string’, ‘null’]) (optional) Alias for ref_base. Reference allele.

  • alt_base ([‘string’, ‘null’]) (optional) Alternate allele (e.g., ‘T’, ‘A’, ‘G’, ‘C’)

  • alt ([‘string’, ‘null’]) (optional) Alias for alt_base. Alternate allele.

  • annotators ([‘string’, ‘null’]) (optional) Comma-separated annotator names (e.g., ‘clinvar,gnomad3,sift,polyphen2,revel,alphamissense’). If omitted, returns only basic variant annotation (gene, consequence). Common annotators: clinvar, gnomad3, sift, polyphen2, cadd_exome, revel, alphamissense, spliceai, dann, fathmm, gerp, phastcons, dbsnp, mutation_assessor, provean, vest, primateai, lrt.

Example Usage:

query = {
    "name": "OpenCRAVAT_annotate_variant",
    "arguments": {
    }
}
result = tu.run(query)

OpenCRAVAT_list_annotators (Type: OpenCRAVATTool)

List all available annotation modules on the OpenCRAVAT server. Returns 182+ annotators including…

OpenCRAVAT_list_annotators tool specification

Tool Information:

  • Name: OpenCRAVAT_list_annotators

  • Type: OpenCRAVATTool

  • Description: List all available annotation modules on the OpenCRAVAT server. Returns 182+ annotators including variant effect predictors (SIFT, PolyPhen-2, REVEL, AlphaMissense), population databases (gnomAD, ExAC), clinical databases (ClinVar, COSMIC), conservation scores (GERP, PhastCons), and more. Optionally filter by category type.

Parameters:

  • category ([‘string’, ‘null’]) (optional) Filter annotators by type/category substring (e.g., ‘annotator’, ‘converter’). Case-insensitive.

Example Usage:

query = {
    "name": "OpenCRAVAT_list_annotators",
    "arguments": {
    }
}
result = tu.run(query)