Cadd Tools

Configuration File: cadd_tools.json Tool Type: Local Tools Count: 3

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

Available Tools

CADD_get_position_scores (Type: CADDTool)

Get CADD scores for all possible substitutions at a genomic position. Returns PHRED scores for A,…

CADD_get_position_scores tool specification

Tool Information:

  • Name: CADD_get_position_scores

  • Type: CADDTool

  • Description: Get CADD scores for all possible substitutions at a genomic position. Returns PHRED scores for A, C, G, T variants at the position. Useful for saturation mutagenesis analysis.

Parameters:

  • chrom (string) (required) Chromosome (1-22, X, Y, MT)

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

  • version (string) (optional) CADD version and genome build

Example Usage:

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

CADD_get_range_scores (Type: CADDTool)

Get CADD scores for all variants in a genomic range (max 100bp). Returns all pre-computed deleter…

CADD_get_range_scores tool specification

Tool Information:

  • Name: CADD_get_range_scores

  • Type: CADDTool

  • Description: Get CADD scores for all variants in a genomic range (max 100bp). Returns all pre-computed deleteriousness scores in the region. Use for hotspot analysis or exon scanning.

Parameters:

  • chrom (string) (required) Chromosome (1-22, X, Y, MT)

  • start (integer) (required) Start position (1-based, inclusive)

  • end (integer) (required) End position (1-based, inclusive). Max range: 100bp.

  • version (string) (optional) CADD version and genome build

Example Usage:

query = {
    "name": "CADD_get_range_scores",
    "arguments": {
        "chrom": "example_value",
        "start": 10,
        "end": 10
    }
}
result = tu.run(query)

CADD_get_variant_score (Type: CADDTool)

Get CADD deleteriousness score for a specific variant. PHRED scores: >=20 top 1% deleterious (pat…

CADD_get_variant_score tool specification

Tool Information:

  • Name: CADD_get_variant_score

  • Type: CADDTool

  • Description: Get CADD deleteriousness score for a specific variant. PHRED scores: >=20 top 1% deleterious (pathogenic threshold ~15-20), >=30 top 0.1%. Input: chromosome, position, ref, alt alleles. Supports GRCh37 and GRCh38.

Parameters:

  • chrom (string) (required) Chromosome (1-22, X, Y, MT). Can include ‘chr’ prefix.

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

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

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

  • version (string) (optional) CADD version and genome build

  • include_annotations (boolean) (optional) Include full annotation details in response

Example Usage:

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