Het Hom Ratio Screen
Screen heterozygous/homozygous-alternate variant ratio against caller-supplied cohort expectations.
Description
The heterozygous-to-homozygous-alternate ratio is a descriptive variant summary.
The heterozygous-to-homozygous-alternate ratio is a descriptive variant summary. Expected ranges can vary with ancestry, assay and filtering.
Screen heterozygous/homozygous-alternate variant ratio against caller-supplied cohort expectations.
When to use Het Hom Ratio Screen
Use this for the following task: Screen heterozygous/homozygous-alternate variant ratio against caller-supplied cohort expectations.
Prepare the caller-filtered sequences, counts, coordinates or annotations requested below. Keep identifiers and paired lists aligned on the same reference.
How to use Het Hom Ratio Screen 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 heterozygousCount, homozygousAlternateCount, minimumRatio, maximumRatio using the field table, then run the tool.
- Read hetHomRatio, withinRange. 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 |
|---|---|---|---|
| heterozygousCount | Heterozygous count | integer; minimum 0 | Required |
| homozygousAlternateCount | Homozygous alternate count | integer; minimum 1 | Required |
| minimumRatio | Minimum ratio | number; minimum 0 | Required |
| maximumRatio | Maximum ratio | number; minimum 0 | Required |
Require nonnegative heterozygous count, positive homozygous-alternate count and ordered nonnegative bounds. Test the ratio inclusively.1
ratio = heterozygousCount/homozygousAlternateCount This summarizes the declared operation. Units, indexing, inclusivity and exceptional cases are explained in the surrounding text.
| Output field | Meaning | Value type |
|---|---|---|
| hetHomRatio | Het hom ratio | number |
| withinRange | Within range | boolean |
{
"input": {
"heterozygousCount": 150,
"homozygousAlternateCount": 100,
"minimumRatio": 1.4,
"maximumRatio": 1.6
},
"output": {
"hetHomRatio": 1.5,
"withinRange": true
}
}Limitations and assumptions
A zero denominator is rejected. The range is supplied and does not establish a universal quality threshold.
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 Transition Transversion Ratio for this operation: Classify substitutions as transitions or transversions and compare Ti/Tv with supplied bounds. 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.
The implementation reference documents the exact calculation, supported input shapes and returned fields.
References
-
Het Hom Ratio Screen — tool.io
Similar or alternative tools
- Transition Transversion Ratio
Classify substitutions as transitions or transversions and compare Ti/Tv with supplied bounds.
- Private Singleton Tally
Identify alternate alleles seen exactly once in the target and absent from all other samples.