Description
Count matching reference/alternate prefixes and remaining suffixes.
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.
Count matching reference/alternate prefixes and remaining suffixes.
When to use this tool
Use VCF Reference Padding Count when checking the stated restricted VCF allele or genotype convention.
How to use the tool and how it works
- Enter reference, alternate. Use the units and conventions below.
- Run the tool. Correct any format, range, or cross-field input error before interpreting the output.
- Read commonPrefix, commonSuffixAfterPrefix. Use the output convention below.
Count matching reference/alternate prefixes and remaining suffixes. Require nonempty A/C/G/T/N strings; compare literal case-sensitive characters, then count suffix matches only outside the matched prefix.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 |
|---|---|---|
| reference | Reference | Required. Text; maximum UTF-16 length 8192. |
| alternate | Alternate | Required. Text; maximum UTF-16 length 8192. |
| Output field | Interpretation | Returned shape |
|---|---|---|
| commonPrefix | Common Prefix | Required. Safe integer. |
| commonSuffixAfterPrefix | Common Suffix After Prefix | Required. Safe integer. |
{
"input": {
"reference": "AT",
"alternate": "A"
},
"output": {
"commonPrefix": 1,
"commonSuffixAfterPrefix": 0
}
}Limitations and assumptions
- This reports common padding without normalizing or left-aligning a variant; lowercase and uppercase bases remain distinct comparisons.
- 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-reference-padding-count — tool.io
-
VCF version 4.5 specification — GA4GH and SAMtools maintainers
Similar or alternative tools
- Bioinformatics: VCF Symbolic Alt Label
Classify one restricted VCF alternate-allele token.
- VCF Break End Orientation Token
Split a restricted VCF breakend token.