VCF Break End Orientation Token Tool

Description

Split a restricted VCF breakend 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.

Split a restricted VCF breakend token.

When to use this tool

Use VCF Break End Orientation Token when checking the stated restricted VCF allele or genotype convention.

How to use the tool and how it works

Enter allele. Use the units and conventions below.
Run the tool. Correct any format, range, or cross-field input error before interpreting the output.
Read remote, bracket, localSequence, sequencePlacement. Use the output convention below.

Split a restricted VCF breakend token. Require matching brackets enclosing ASCII contig:positive-position and sequence on exactly one side; return remote locus, bracket, local sequence and placement before or after remote.^[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
allele	Allele	Required. Text; maximum UTF-16 length 8192.

Output field	Interpretation	Returned shape
remote	Restricted contig:positive-position string, without genomic reference lookup.	Required. Text; maximum UTF-16 length 8192.
bracket	Bracket	Required. Text; maximum UTF-16 length 8192.
localSequence	Local Sequence	Required. Text; maximum UTF-16 length 8192.
sequencePlacement	Sequence Placement	Required. Text; maximum UTF-16 length 8192.

json

{
  "input": {
    "allele": "A]chr1:10]"
  },
  "output": {
    "remote": "chr1:10",
    "bracket": "]",
    "localSequence": "A",
    "sequencePlacement": "before-remote"
  }
}

Limitations and assumptions

This is restricted lexical parsing, not breakpoint validation, reference lookup, all VCF breakend forms or a biological rearrangement interpretation.
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-break-end-orientation-token — 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.
Bioinformatics: VCF Symbolic Alt Label
Classify one restricted VCF alternate-allele token.