Cancervar Tools

Configuration File: cancervar_tools.json Tool Type: Local Tools Count: 1

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

Available Tools

CancerVar_classify_variant (Type: CancerVarTool)

Classify a somatic cancer variant using AMP/ASCO/CAP 2017 guidelines (CancerVar). Returns a Tier …

CancerVar_classify_variant tool specification

Tool Information:

  • Name: CancerVar_classify_variant

  • Type: CancerVarTool

  • Description: Classify a somatic cancer variant using AMP/ASCO/CAP 2017 guidelines (CancerVar). Returns a Tier I–IV assignment: Tier I = Strong Clinical Significance (FDA-approved therapy association), Tier II = Potential Clinical Significance (investigational/preclinical evidence), Tier III = Unknown Clinical Significance, Tier IV = Benign/Likely Benign. Also returns 12 CBP evidence scores and an Oncogenicity Pathogenicity Index (OPAI, 0–1). Input requires genomic coordinates in hg19 or hg38. No API key needed. Example: BRAF V600E (chr7:140453136 A>T hg19) is Tier I (strong) with OPAI=0.99.

Parameters:

  • chrom (string) (required) Chromosome number or name. Can include ‘chr’ prefix (e.g., ‘7’, ‘chr7’, ‘X’).

  • pos (integer) (required) Genomic position (1-based).

  • ref (string) (required) Reference allele (e.g., ‘A’, ‘G’, ‘ATCG’).

  • alt (string) (required) Alternate allele (e.g., ‘T’, ‘C’).

  • build (string) (optional) Genome build. Default: hg19.

Example Usage:

query = {
    "name": "CancerVar_classify_variant",
    "arguments": {
        "chrom": "example_value",
        "pos": 10,
        "ref": "example_value",
        "alt": "example_value"
    }
}
result = tu.run(query)