Trans Heterozygote Pairs

Find known trans-phased heterozygous variant pairs within each gene; not a pathogenicity classification.

Description

Two heterozygous variants in one gene can lie on the same or different haplotypes.

Two heterozygous variants in one gene can lie on the same or different haplotypes. Known trans phase means their alternate alleles lie on different supplied haplotypes.

Find known trans-phased heterozygous variant pairs within each gene; not a pathogenicity classification.

When to use Trans Heterozygote Pairs

Use this for the following task: Find known trans-phased heterozygous variant pairs within each gene; not a pathogenicity classification.

Prepare the caller-filtered sequences, counts, coordinates or annotations requested below. Keep identifiers and paired lists aligned on the same reference.

How to use Trans Heterozygote Pairs 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, geneIds, phasedAlternateHaplotypes using the field table, then run the tool.
Read firstVariants, secondVariants, pairGenes. 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 400; each entry: string; minimum text length 1; maximum text length 1000000; pattern \S	Required
geneIds	Gene ids	list of string; minimum entries 0; maximum entries 400; each entry: string; minimum text length 1; maximum text length 1000000; pattern \S	Required
phasedAlternateHaplotypes	Phased alternate haplotypes	list of integer; minimum entries 0; maximum entries 400; each entry: integer; minimum 0; maximum 1	Required

Align distinct variant IDs with genes and supported haplotype labels. Compare all ordered index pairs and emit variant and gene lists for qualifying pairs.^[1]

emit pair (i,j) when i<j, same gene and different known haplotypes

This summarizes the declared operation. Units, indexing, inclusivity and exceptional cases are explained in the surrounding text.

Output field	Meaning	Value type
firstVariants	First variants	list of string
secondVariants	Second variants	list of string
pairGenes	Pair genes	list of string

json

{
  "input": {
    "variantIds": [
      "v1",
      "v2",
      "v3"
    ],
    "geneIds": [
      "A",
      "A",
      "B"
    ],
    "phasedAlternateHaplotypes": [
      0,
      1,
      0
    ]
  },
  "output": {
    "firstVariants": [
      "v1"
    ],
    "secondVariants": [
      "v2"
    ],
    "pairGenes": [
      "A"
    ]
  }
}

Limitations and assumptions

Phase is supplied, not inferred. This does not classify pathogenicity or establish a recessive molecular diagnosis.

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 Homozygous LOF Burden for this operation: Tally caller-annotated homozygous loss-of-function variants per gene.

The implementation reference documents the exact calculation, supported input shapes and returned fields.

References

Trans Heterozygote Pairs — tool.io

Similar or alternative tools

Trio Mendelian Check
Check diploid trio Mendelian inheritance and identify absent-parent alternate allele candidates.
Homozygous LOF Burden
Tally caller-annotated homozygous loss-of-function variants per gene.