Indel Density
Compute insertion-plus-deletion variant density per callable kilobase.
Description
Indel density normalizes insertion and deletion event counts to callable territory.
Indel density normalizes insertion and deletion event counts to callable territory. It counts events rather than total inserted or deleted bases.
Compute insertion-plus-deletion variant density per callable kilobase.
When to use Indel Density
Use this for the following task: Compute insertion-plus-deletion variant density per callable kilobase.
Prepare the caller-filtered sequences, counts, coordinates or annotations requested below. Keep identifiers and paired lists aligned on the same reference.
How to use Indel Density 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 insertionCount, deletionCount, callableBases using the field table, then run the tool.
- Read totalIndels, indelsPerKilobase. 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 |
|---|---|---|---|
| insertionCount | Insertion count | integer; minimum 0 | Required |
| deletionCount | Deletion count | integer; minimum 0 | Required |
| callableBases | Callable bases | integer; minimum 1 | Required |
Use nonnegative counts and positive callable bases. Require the combined count to fit the safe integer range, then normalize.1
total = insertionCount+deletionCount; per kb = 1000 total/callableBases This summarizes the declared operation. Units, indexing, inclusivity and exceptional cases are explained in the surrounding text.
| Output field | Meaning | Value type |
|---|---|---|
| totalIndels | Total indels | integer |
| indelsPerKilobase | Indels per kilobase | number |
{
"input": {
"insertionCount": 10,
"deletionCount": 5,
"callableBases": 10000
},
"output": {
"totalIndels": 15,
"indelsPerKilobase": 1.5
}
}Limitations and assumptions
Variant filtering and callable intervals are external; no allele length or clinical impact is analyzed.
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 Tumor Mutation Burden for this operation: Normalize caller-filtered somatic mutation count to callable target megabases. 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
-
Indel Density — tool.io
Similar or alternative tools
- Tumor Mutation Burden
Normalize caller-filtered somatic mutation count to callable target megabases.
- Localized SNP Density
Find SNP-anchored half-open windows meeting a caller-defined localized density threshold.