Forge Tools cadd_scores

cadd_scores read

scidex.forge.cadd_scores

Score human genomic variants with CADD (Combined Annotation Dependent Depletion) from cadd.gs.washington.edu. Returns phred-scaled pathogenicity estimates — PHRED>20 indicates top 1% most deleterious variants; PHRED>30 top 0.1%. Accepts variants in 'chr:pos:ref:alt' format (e.g. '1:15211522:A:T'). Supports GRCh38 (default) and GRCh37. Fills the gap between gnomAD (frequency) and ClinVar (curated classification) with a computational deleteriousness score applicable to any variant. Returns variants_scored list with phred, raw_score, and optional consequence. not_found=True when no variants could be scored. API: CADD REST API v1.0 (cadd.gs.washington.edu) — public, no authentication required.

HTTP: POST /api/scidex/forge/cadd_scores

Invoke

Calls scidex.tool.invoke on the substrate with this tool name. Edit the JSON below — it must match the input schema. The substrate runs the tool, records the call in substrate_tool_calls, and returns a structured envelope.

Sign in to invoke this tool. Schema and curl snippet are visible to anyone.

Schemas

Input schema 
{
  "additionalProperties": false,
  "description": "Input schema for ``scidex.forge.cadd_scores``.",
  "properties": {
    "variants": {
      "description": "Variants to score, each in 'chr:pos:ref:alt' format (e.g. '1:15211522:A:T' or 'chr1:15211522:A:T'). At most 50 variants per request.",
      "items": {
        "type": "string"
      },
      "maxItems": 50,
      "minItems": 1,
      "title": "Variants",
      "type": "array"
    },
    "genome_build": {
      "default": "GRCh38",
      "description": "Reference genome assembly. 'GRCh38' (hg38, default) or 'GRCh37' (hg19). Affects which CADD model and coordinate space is used.",
      "enum": [
        "GRCh38",
        "GRCh37"
      ],
      "title": "Genome Build",
      "type": "string"
    }
  },
  "required": [
    "variants"
  ],
  "title": "ForgeCaddScoresIn",
  "type": "object"
}
Output schema 
{
  "$defs": {
    "CaddScore": {
      "description": "CADD score record for one variant.",
      "properties": {
        "chromosome": {
          "description": "Chromosome identifier (e.g. '1', 'X', 'MT').",
          "title": "Chromosome",
          "type": "string"
        },
        "position": {
          "description": "1-based genomic position.",
          "title": "Position",
          "type": "integer"
        },
        "ref": {
          "description": "Reference allele.",
          "title": "Ref",
          "type": "string"
        },
        "alt": {
          "description": "Alternate allele.",
          "title": "Alt",
          "type": "string"
        },
        "phred": {
          "description": "CADD PHRED-scaled score. >20 = top 1% most deleterious; >30 = top 0.1%. Practical range: 0–99.",
          "title": "Phred",
          "type": "number"
        },
        "raw_score": {
          "description": "CADD raw SVM score (pre-PHRED-scaling). Negative = likely benign.",
          "title": "Raw Score",
          "type": "number"
        },
        "consequence": {
          "anyOf": [
            {
              "type": "string"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "description": "Variant consequence annotation if returned by the API.",
          "title": "Consequence"
        }
      },
      "required": [
        "chromosome",
        "position",
        "ref",
        "alt",
        "phred",
        "raw_score"
      ],
      "title": "CaddScore",
      "type": "object"
    }
  },
  "description": "Response shape for ``scidex.forge.cadd_scores``.",
  "properties": {
    "variants_scored": {
      "description": "CADD scores for successfully annotated variants.",
      "items": {
        "$ref": "#/$defs/CaddScore"
      },
      "title": "Variants Scored",
      "type": "array"
    },
    "not_found": {
      "description": "True when no variants in the request could be scored.",
      "title": "Not Found",
      "type": "boolean"
    },
    "total_requested": {
      "description": "Number of variants submitted for scoring.",
      "title": "Total Requested",
      "type": "integer"
    },
    "total_scored": {
      "description": "Number of variants successfully scored.",
      "title": "Total Scored",
      "type": "integer"
    },
    "source": {
      "default": "CADD (cadd.gs.washington.edu)",
      "description": "Data source attribution.",
      "title": "Source",
      "type": "string"
    }
  },
  "required": [
    "not_found",
    "total_requested",
    "total_scored"
  ],
  "title": "ForgeCaddScoresOut",
  "type": "object"
}

curl snippet

Replace $SCIDEX_JWT with a valid bearer token. Read verbs are usually accessible without auth in dev; production requires a JWT.

curl -sS -X POST '/api/scidex/forge/cadd_scores' \
  -H 'authorization: Bearer $SCIDEX_JWT' \
  -H 'content-type: application/json' \
  -d '{
  "variants": []
}'

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