Trio Mendelian Check
Check diploid trio Mendelian inheritance and identify absent-parent alternate allele candidates.
Description
A diploid child normally receives one allele from each parent.
A diploid child normally receives one allele from each parent. A child alternate allele absent from both supplied parent genotypes is a candidate for further review.1
Check diploid trio Mendelian inheritance and identify absent-parent alternate allele candidates.
When to use Trio Mendelian Check
Use this for the following task: Check diploid trio Mendelian inheritance and identify absent-parent alternate allele candidates.
Prepare the caller-filtered sequences, counts, coordinates or annotations requested below. Keep identifiers and paired lists aligned on the same reference.
How to use Trio Mendelian Check 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 motherGenotypes, fatherGenotypes, childGenotypes using the field table, then run the tool.
- Read violationIndexes, denovoCandidateIndexes, consistentCount. 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 |
|---|---|---|---|
| motherGenotypes | Mother genotypes | list of string; minimum entries 1; maximum entries 100000; each entry: string; minimum text length 3; maximum text length 1000000; pattern ^[0-9]+[|/][0-9]+(?![\s\S]) | Required |
| fatherGenotypes | Father genotypes | list of string; minimum entries 1; maximum entries 100000; each entry: string; minimum text length 3; maximum text length 1000000; pattern ^[0-9]+[|/][0-9]+(?![\s\S]) | Required |
| childGenotypes | Called diploid VCF allele indexes separated by / or |; missing calls are invalid. Phase is ignored for inheritance. | list of string; minimum entries 1; maximum entries 100000; each entry: string; minimum text length 3; maximum text length 1000000; pattern ^[0-9]+[|/][0-9]+(?![\s\S]) | Required |
Align supported diploid numeric-index genotypes, split / or | and canonicalize leading zeros without converting allele labels to numbers. Return zero-based violation and absent-parent alternate candidate indices.2
consistent = either parental assignment matches the two child alleles This summarizes the declared operation. Units, indexing, inclusivity and exceptional cases are explained in the surrounding text.
| Output field | Meaning | Value type |
|---|---|---|
| violationIndexes | Violation indexes | list of integer |
| denovoCandidateIndexes | Denovo candidate indexes | list of integer |
| consistentCount | Consistent count | integer |
{
"input": {
"motherGenotypes": [
"0/0",
"0/1"
],
"fatherGenotypes": [
"0/0",
"0/0"
],
"childGenotypes": [
"0/1",
"0/1"
]
},
"output": {
"violationIndexes": [
0
],
"denovoCandidateIndexes": [
0
],
"consistentCount": 1
}
}Limitations and assumptions
Missing calls, sex-chromosome inheritance and genotype quality need separate handling. A candidate is not proof of a de novo event.
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 VCF Record Audit for this operation: Audit VCF record field count and essential fields for the supplied number of samples. For a complementary task, use Private Singleton Tally for this operation: Identify alternate alleles seen exactly once in the target and absent from all other samples.
Further background: Background specification: Trio Mendelian Check.
References
-
Background specification: Trio Mendelian Check — GA4GH / HTS specifications
-
Trio Mendelian Check — tool.io
Similar or alternative tools
- VCF Record Audit
Audit VCF record field count and essential fields for the supplied number of samples.
- Private Singleton Tally
Identify alternate alleles seen exactly once in the target and absent from all other samples.