Description
Return allele count, missingness and phasing from a genotype 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.
Return allele count, missingness and phasing from a genotype token.
When to use this tool
Use VCF Missing Genotype Ploidy Token when checking the stated restricted VCF allele or genotype convention.
How to use the tool and how it works
- Enter genotype. Use the units and conventions below.
- Run the tool. Correct any format, range, or cross-field input error before interpreting the output.
- Read ploidy, allMissing, partiallyMissing, phased. Inspect allMissing, partiallyMissing, phased before interpreting the associated values.
Return allele count, missingness and phasing from a genotype token. Accept decimal indexes or dots separated by slash/pipe, at most 256 alleles; allMissing/partiallyMissing count dots, phased requires multiple alleles with pipes and no slash.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 |
|---|---|---|
| genotype | Genotype | Required. Text; maximum UTF-16 length 8192. |
| Output field | Interpretation | Returned shape |
|---|---|---|
| ploidy | Ploidy | Required. Safe integer. |
| allMissing | All Missing | Required. Boolean. |
| partiallyMissing | Partially Missing | Required. Boolean. |
| phased | Multiple alleles, at least one pipe and no slash; missing alleles are still counted. | Required. Boolean. |
{
"input": {
"genotype": "./."
},
"output": {
"ploidy": 2,
"allMissing": true,
"partiallyMissing": false,
"phased": false
}
}Limitations and assumptions
- Mixed separators are accepted but not labeled fully phased; allele indexes, sample ploidy and complete VCF validity are not verified.
- 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-missing-genotype-ploidy-token — tool.io
-
VCF version 4.5 specification — GA4GH and SAMtools maintainers
Similar or alternative tools
- Phased Genotype Missing Count
Count missing alleles in a restricted genotype token.
- VCF Allele Index Reference Alternate Token
Resolve a supplied VCF allele index.