CADD-like Combined Deleteriousness Score Threshold Gate Checker
Screen a caller-supplied CADD-like score and threshold; does not calculate CADD or infer pathogenicity.
Description
Screen a caller-supplied CADD-like score and threshold; does not calculate CADD or infer pathogenicity.
A score threshold can screen a prediction without proving that a variant causes disease. Keeping a signed margin alongside the pass flag exposes how far it lies from the supplied boundary.
When to use this tool
Screen a caller-supplied CADD-like score and threshold; does not calculate CADD or infer pathogenicity.
- Prepare the supplied score, callerThreshold fields for this operation.
- Compare the complete example with the representation used by your own input before carrying the result into another step.
How to use the tool and how it works
- Enter score, callerThreshold. Use the exact text syntax, units and index conventions explained below.
- Run the tool. If input validation fails, correct the supplied fields before interpreting any result.
- Read result.signedMargin, result.atOrAboveThreshold, result.pathogenicityEstablished. Interpret false, null and empty lists using the distinctions below; they can be valid outputs.
Return score-callerThreshold and whether score is at least callerThreshold. Always return pathogenicityEstablished false.1
| Input field | Meaning and representation | Accepted input |
|---|---|---|
| score | score. | Finite number |
| callerThreshold | caller threshold. | Finite number |
| Output field | Interpretation |
|---|---|
| result | Object containing the named outputs below. |
| result.signedMargin | The signed margin value under the stated formula or text convention. |
| result.atOrAboveThreshold | Flag for at or above threshold under the exact condition described above. |
| result.pathogenicityEstablished | Always false: a numerical score gate does not establish clinical pathogenicity. |
{
"input": {
"score": 20,
"callerThreshold": 15
},
"output": {
"result": {
"signedMargin": 5,
"atOrAboveThreshold": true,
"pathogenicityEstablished": false
}
}
}Limitations and assumptions
- The tool does not identify the scoring system, justify the threshold or combine clinical evidence. Equality passes, and arbitrary finite scores are not automatically comparable across models.
- Every declared top-level field is required and unexpected fields are rejected. Numeric inputs must be finite; ordinary text fields are bounded to 8,192 UTF-16 code units, with tighter operation-specific limits where stated.
- Ordinary string lists have at most 128 entries of at most 128 code units each; numeric lists and matrices have separate bounded size checks. Nonfinite results and excessively large serialized outputs are rejected.
- Indexes are zero-based and spans have an exclusive end unless explicitly stated otherwise. A valid false, null or empty-list result is distinct from malformed input.
Alternative or Complementary methods
Retain the reference assembly, accession/version and measurement convention with an analysis. Length summaries, flags and lookup notes do not validate an assembly or classify a variant; use the corresponding sequence, alignment or evidence-review workflow.
References
Similar or alternative tools
- alignment identity gate
Alignment identity depends on which columns count in the denominator.
- Duplicated Fragmentation Warning Completeness Caveat Flag Checker
Flag supplied complete-duplicated and fragmented ortholog evidence; not a BUSCO run or proof of contamination/assembly failure.