Pharmacogenomic Assay Covered Variant Check Tool

Description

Audit explicitly supplied assay-coverage IDs without predicting assay sensitivity.

Pharmacogenomic records distinguish allele labels, copy counts, reference-sequence versions, coordinate systems, and evidence about chromosome phase. A balanced count or matching token can check a record without establishing the underlying genotype. Supplied activity values and interpretation rules remain separate from a current gene-specific clinical guideline.

Audit explicitly supplied assay-coverage IDs without predicting assay sensitivity.

When to use this tool

Use Pharmacogenomic Assay Covered Variant Check when you need this specific allele-token, reference-coordinate, copy-budget, or source-support check.

How to use the tool and how it works

Enter requested, covered, excluded. Keep parallel arrays aligned. Use the units and conventions below.
Run the tool. Correct any format, range, or cross-field input error before interpreting the output.
Read coveredRequested, uncovered, explicitlyExcluded. Use the output convention below.

Require requested tokens to be unique. Return coveredRequested for tokens present in covered and absent from excluded, uncovered for tokens absent from covered, and explicitlyExcluded for tokens present in excluded.^[1]

Input field	Meaning and units	Accepted input
requested	Requested	Required. Array of text; maximum UTF-16 length 8192; maximum items 256.
covered	Covered	Required. Array of text; maximum UTF-16 length 8192; maximum items 256.
excluded	Excluded	Required. Array of text; maximum UTF-16 length 8192; maximum items 256.

Output field	Interpretation	Returned shape
coveredRequested	Covered Requested	Required. Array of text; maximum UTF-16 length 8192; maximum items 256.
uncovered	Uncovered	Required. Array of text; maximum UTF-16 length 8192; maximum items 256.
explicitlyExcluded	Explicitly Excluded	Required. Array of text; maximum UTF-16 length 8192; maximum items 256.

json

{
  "input": {
    "requested": [
      "A",
      "B",
      "C"
    ],
    "covered": [
      "A",
      "B"
    ],
    "excluded": [
      "B"
    ]
  },
  "output": {
    "coveredRequested": [
      "A"
    ],
    "uncovered": [
      "C"
    ],
    "explicitlyExcluded": [
      "B"
    ]
  }
}

Limitations and assumptions

Excluded and uncovered lists can overlap. The supplied coverage lists are trusted, use exact token matching, and do not establish analytical sensitivity or a complete genotype call.
Inputs must satisfy both the field types and the cross-field conditions above. Invalid input causes an error; a successful false flag or documented placeholder is a different result.

Alternative or Complementary methods

Use a current gene-specific nomenclature and a validated interpretation process when allele identity, phase, function, or clinical decisions matter. Verify source versions and reference coordinates before combining records.

References

Calculation and input contract: pharmacogenomics/pharmacogenomic-assay-covered-variant-check — tool.io

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