Structural Variant Size Bands
Classify structural variant sizes using caller-specified base-pair boundaries.
Description
Variant size bands provide a consistent way to group events for a particular analysis.
Variant size bands provide a consistent way to group events for a particular analysis. Cutoffs are analysis choices rather than proof of a variant’s mechanism.
Classify structural variant sizes using caller-specified base-pair boundaries.
When to use Structural Variant Size Bands
Use this for the following task: Classify structural variant sizes using caller-specified base-pair boundaries.
Prepare the caller-filtered sequences, counts, coordinates or annotations requested below. Keep identifiers and paired lists aligned on the same reference.
How to use Structural Variant Size Bands 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 variantSizesBp, svMinimumBp, largeVariantMinimumBp using the field table, then run the tool.
- Read sizeClasses. 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 |
|---|---|---|---|
| variantSizesBp | Variant sizes bp | list of integer; minimum entries 1; maximum entries 100000; each entry: integer; minimum 0 | Required |
| svMinimumBp | Sizes at this inclusive boundary enter the structural class. | integer; minimum 1 | Required |
| largeVariantMinimumBp | Sizes at this inclusive boundary enter the large class; must exceed svMinimumBp. | integer; minimum 1 | Required |
Supply nonnegative integer sizes and positive ordered cutoffs. Classify each size preserving input order; equality belongs to the higher band.1
small: size < svMinimum; structural: svMinimum ≤ size < largeMinimum; large-structural: size ≥ largeMinimum This summarizes the declared operation. Units, indexing, inclusivity and exceptional cases are explained in the surrounding text.
| Output field | Meaning | Value type |
|---|---|---|
| sizeClasses | Size classes | list of string |
{
"input": {
"variantSizesBp": [
10,
100,
2000000
],
"svMinimumBp": 50,
"largeVariantMinimumBp": 1000000
},
"output": {
"sizeClasses": [
"small",
"structural",
"large-structural"
]
}
}Limitations and assumptions
No fixed universal cutoffs are embedded. The tool does not detect variants or interpret pathogenicity.
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 Indel Density for this operation: Compute insertion-plus-deletion variant density per callable kilobase. For a complementary task, use Localized SNP Density for this operation: Find SNP-anchored half-open windows meeting a caller-defined localized density threshold.
The implementation reference documents the exact calculation, supported input shapes and returned fields.
References
-
Structural Variant Size Bands — tool.io
Similar or alternative tools
- Indel Density
Compute insertion-plus-deletion variant density per callable kilobase.
- Localized SNP Density
Find SNP-anchored half-open windows meeting a caller-defined localized density threshold.