Bioinformatics: VCF Symbolic Alt Label Tool

Description

Classify one restricted VCF alternate-allele token.

VCF represents reference/alternate alleles and sample genotypes with distinct tokens for sequence, symbolic variants, missing values and phasing. A restricted token parser can expose one part of that notation without validating the header, allele relationships, sample ploidy or the whole variant record.

Classify one restricted VCF alternate-allele token.

When to use this tool

Use Bioinformatics: VCF Symbolic Alt Label when checking the stated restricted VCF allele or genotype convention.

How to use the tool and how it works

Enter alt. Use the units and conventions below.
Run the tool. Correct any format, range, or cross-field input error before interpreting the output.
Read result. Expand result to inspect the returned fields.

Classify one restricted VCF alternate-allele token. Accept a bracketed ASCII symbolic identifier, asterisk, or nonempty A/C/G/T/N sequence; symbolic returns its inner identifier, spanningDeletion tests asterisk, otherwise identifier is empty.^[1]

VCF distinguishes allele representations, missing values and genotype separators. This helper implements only the restricted token operation described above, rather than full-file or biological validation.^[2]

Input field	Meaning and units	Accepted input
alt	Alt	Required. Text. Implementation limit: 8192 Unicode code points and 16384 UTF-16 code units.

Output field	Interpretation	Returned shape
result	Returned calculated value or nested object under the stated output convention.	Required. Object.
result.symbolic	Symbolic	Calculated result member: boolean.
result.identifier	Inner symbolic label or empty string for a sequence/asterisk token.	Calculated result member: string.
result.spanningDeletion	Spanning Deletion	Calculated result member: boolean.

json

{
  "input": {
    "alt": "\u003cDEL>"
  },
  "output": {
    "result": {
      "symbolic": true,
      "identifier": "DEL",
      "spanningDeletion": false
    }
  }
}

Limitations and assumptions

Breakends and other VCF constructs are outside this grammar; a valid token is not a complete VCF record or verified variant.
Outputs are nested inside result. 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

Validate the complete file against the intended VCF version and reference, and use appropriate variant normalization or interpretation methods for biological conclusions.

References

Calculation and input contract: bioinformatics/vcf-symbolic-alt-label — tool.io
VCF version 4.5 specification — GA4GH and SAMtools maintainers

Similar or alternative tools

VCF Reference Padding Count
Count matching reference/alternate prefixes and remaining suffixes.
VCF Break End Orientation Token
Split a restricted VCF breakend token.