Genotype Call Allele Count Tool

Description

Count supplied allele-call tokens without calling variants, assigning phase or predicting drug response.

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.

Count supplied allele-call tokens without calling variants, assigning phase or predicting drug response.

When to use this tool

Use Genotype Call Allele Count 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 alleles, missingTokens. 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 calledCount, missingCount, distinctCalledAlleles. Use the output convention below.

Remove alleles matching any missingTokens entry. Return calledCount, missingCount, and distinctCalledAlleles by exact string identity.^[1]

Input field	Meaning and units	Accepted input
alleles	Alleles	Required. Array of text; maximum UTF-16 length 8192; maximum items 256.
missingTokens	Missing Tokens	Required. Array of text; maximum UTF-16 length 8192; maximum items 256.

Output field	Interpretation	Returned shape
calledCount	Called Count	Required. Safe integer.
missingCount	Missing Count	Required. Safe integer.
distinctCalledAlleles	Distinct Called Alleles	Required. Safe integer.

json

{
  "input": {
    "alleles": [
      "*1",
      "*2",
      "?"
    ],
    "missingTokens": [
      "?"
    ]
  },
  "output": {
    "calledCount": 2,
    "missingCount": 1,
    "distinctCalledAlleles": 2
  }
}

Limitations and assumptions

Repeated calls count separately but distinct alleles are deduplicated. Tokens are not parsed into variants or copy numbers, and the counts alone do not establish zygosity or a validated genotype.
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/genotype-call-allele-count — tool.io

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