Tumor Mutation Burden

Normalize caller-filtered somatic mutation count to callable target megabases.

Description

Tumor mutation burden normalizes a selected somatic mutation count by callable target size.

Tumor mutation burden normalizes a selected somatic mutation count by callable target size. Changing the callable denominator or inclusion rules changes the result.

Normalize caller-filtered somatic mutation count to callable target megabases.

When to use Tumor Mutation Burden

Use this for the following task: Normalize caller-filtered somatic mutation count to callable target megabases.

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

How to use Tumor Mutation Burden 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 eligibleSomaticMutations, callableTargetBases using the field table, then run the tool.
Read mutationsPerMegabase. 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
eligibleSomaticMutations	Count of caller-filtered eligible somatic mutations.	integer; minimum 0	Required
callableTargetBases	Callable target bases	integer; minimum 1	Required

Use a nonnegative eligible mutation count and positive callable base count from the same assay. Divide by callable megabases.^[1]

mutations per Mb = eligibleMutations/(callableBases/1000000)

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

Output field	Meaning	Value type
mutationsPerMegabase	Mutations per megabase	number

json

{
  "input": {
    "eligibleSomaticMutations": 100,
    "callableTargetBases": 10000000
  },
  "output": {
    "mutationsPerMegabase": 10
  }
}

Limitations and assumptions

Filtering eligibility is supplied externally. This calculation does not identify somatic variants, select a clinical cutoff or predict treatment response.

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 Callable Depth Fraction for this operation: Calculate callable-base percentage from a depth histogram and minimum calling depth. For a complementary task, use Indel Density for this operation: Compute insertion-plus-deletion variant density per callable kilobase.

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

References

Tumor Mutation Burden — tool.io

Similar or alternative tools

Callable Depth Fraction
Calculate callable-base percentage from a depth histogram and minimum calling depth.
Indel Density
Compute insertion-plus-deletion variant density per callable kilobase.