VCF Genotype Allele Separator Flag

Description

Inspect allele tokens and phasing separators in a supplied genotype token.

Sequence formats distinguish coordinate origins, included endpoints, allele separators and identifier grammars. A genomic interbase position differs from a base number, and a parsed optional-field value may still violate its declared type. Local token checks preserve representation without validating a complete file, sequence, reference assembly or biological interpretation.

Inspect allele tokens and phasing separators in a supplied genotype token.

When to use this tool

Use VCF Genotype Allele Separator Flag when you already have genotypeToken and need to inspect allele tokens and phasing separators in a supplied genotype token.

How to use the tool and how it works

Enter genotypeToken. Use the units and conventions below.
Run the tool. Correct any format, range, or cross-field input error before interpreting the output.
Read alleleTokens, separators, hasPhasedSeparator, hasUnphasedSeparator. Inspect hasPhasedSeparator, hasUnphasedSeparator before interpreting the associated values.

Accept digit strings or . alleles separated by / or |, optionally preceded by one / or |. Strip that leading separator only for allele splitting; return all separator characters and flags for either kind.^[1]

Genotype allele notation uses allele indices or missing-allele markers with separators describing phasing relationships. A separator-presence flag is narrower than validating alleles, phase information and the surrounding variant record.^[2]

Input field	Meaning and units	Accepted input
genotypeToken	Allele digit strings or . separated by / or \|; one leading separator and mixed separator types are accepted.	Required. Text; maximum UTF-16 length 8192.

Output field	Interpretation	Returned shape
alleleTokens	Allele Tokens	Required. Array of text; maximum UTF-16 length 8192; maximum items 256.
separators	Separators	Required. Array of text; maximum UTF-16 length 8192; maximum items 256.
hasPhasedSeparator	True if any \| occurs, including a leading separator; not proof of fully phased genotype.	Required. Boolean.
hasUnphasedSeparator	Has Unphased Separator	Required. Boolean.

json

{
  "input": {
    "genotypeToken": "0|1"
  },
  "output": {
    "alleleTokens": [
      "0",
      "1"
    ],
    "separators": [
      "|"
    ],
    "hasPhasedSeparator": true,
    "hasUnphasedSeparator": false
  }
}

Limitations and assumptions

Mixed separators and leading zeros are accepted. A phased-separator flag does not establish fully phased alleles; ploidy, allele bounds, missingness interpretation and a complete VCF record are not validated.
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 the complete applicable file specification and a full format validator for conformance. Verify reference assembly, sequence bounds, annotation and database context before interpreting local fields or coordinate transformations.

References

Calculation and input contract: bioinformatics/vcf-genotype-allele-separator-flag — tool.io
Variant Call Format Specification, VCF 4.5 — VCF/BCF specification maintainers

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