Private Singleton Tally
Identify alternate alleles seen exactly once in the target and absent from all other samples.
Description
A private singleton has one alternate copy in the target and none in the comparison samples.
A private singleton has one alternate copy in the target and none in the comparison samples. The comparison set controls whether an allele is private.
Identify alternate alleles seen exactly once in the target and absent from all other samples.
When to use Private Singleton Tally
Use this for the following task: Identify alternate alleles seen exactly once in the target and absent from all other samples.
Prepare the caller-filtered sequences, counts, coordinates or annotations requested below. Keep identifiers and paired lists aligned on the same reference.
How to use Private Singleton Tally and understand its results
- Prepare the caller-filtered sequences, counts, coordinates or annotations requested below. Keep identifiers and paired lists aligned on the same reference.
- Enter variantIds, targetAlternateDosages, otherSampleAlternateAlleles using the field table, then run the tool.
- Read privateSingletonIds, singletonCount. Interpret flags, units, ordering and placeholder values using the rules below.
- Review any reported issue or failed check, correct the supplied values when appropriate, and verify the result in its intended context.
| Input field | Meaning | Value type and bounds | Requirement |
|---|---|---|---|
| variantIds | Variant ids | list of string; minimum entries 0; maximum entries 100000; each entry: string; minimum text length 1; maximum text length 1000000; pattern \S | Required |
| targetAlternateDosages | Target alternate dosages | list of integer; minimum entries 0; maximum entries 100000; each entry: integer; minimum 0; maximum 2 | Required |
| otherSampleAlternateAlleles | Other sample alternate alleles | list of integer; minimum entries 0; maximum entries 100000; each entry: integer; minimum 0 | Required |
Align distinct variant IDs with supported nonnegative target dosages and other-sample counts. Preserve input order and tally qualifying IDs.1
private singleton = targetDosage == 1 AND otherSampleAlternateAlleles == 0 This summarizes the declared operation. Units, indexing, inclusivity and exceptional cases are explained in the surrounding text.
| Output field | Meaning | Value type |
|---|---|---|
| privateSingletonIds | Private singleton ids | list of string |
| singletonCount | Singleton count | integer |
{
"input": {
"variantIds": [
"v1",
"v2",
"v3"
],
"targetAlternateDosages": [
1,
2,
1
],
"otherSampleAlternateAlleles": [
0,
0,
2
]
},
"output": {
"privateSingletonIds": [
"v1"
],
"singletonCount": 1
}
}Limitations and assumptions
Callability, sequencing errors and relatedness are not assessed. Absent calls must not automatically be interpreted as observed zero.
The tool operates on supplied local data; alignment, filtering and annotation must already be appropriate for the stated calculation. Malformed requests produce input errors. A successfully evaluated request can still contain false flags, empty result lists or a result outside the supplied threshold; those outcomes have the meanings stated above.
Alternative or Complementary methods
Choose Trio Mendelian Check for this operation: Check diploid trio Mendelian inheritance and identify absent-parent alternate allele candidates. For a complementary task, use Novel Variant Fraction for this operation: Calculate variants absent from a supplied reference ID set; requires harmonized variant representation.
The implementation reference documents the exact calculation, supported input shapes and returned fields.
References
-
Private Singleton Tally — tool.io
Similar or alternative tools
- Trio Mendelian Check
Check diploid trio Mendelian inheritance and identify absent-parent alternate allele candidates.
- Novel Variant Fraction
Calculate variants absent from a supplied reference ID set; requires harmonized variant representation.