Zero Coverage Targets

Tally target intervals with zero covered bases from supplied per-target coverage summaries.

Description

Target coverage summaries distinguish complete absence of observed coverage from partial coverage.

Target coverage summaries distinguish complete absence of observed coverage from partial coverage. A zero-coverage target contributes its entire interval length to the missing-base total.

Tally target intervals with zero covered bases from supplied per-target coverage summaries.

When to use Zero Coverage Targets

Use this for the following task: Tally target intervals with zero covered bases from supplied per-target coverage summaries.

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

How to use Zero Coverage Targets 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 targetNames, targetBases, coveredBases using the field table, then run the tool.
Read missingTargets, missingTargetBases, missingTargetCount. 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
targetNames	Target names	list of string; each entry: string	Required
targetBases	Target bases	list of number; each entry: number	Required
coveredBases	Covered bases	list of number; each entry: number	Required

Align distinct target names with positive lengths and covered-base counts no greater than each length. Preserve target order in the missing list and tally lengths.^[1]

missing = targets with coveredBases == 0; missingBases = Σ their targetBases

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

Output field	Meaning	Value type
missingTargets	Missing targets	list of string
missingTargetBases	Missing target bases	integer
missingTargetCount	Missing target count	integer

json

{
  "input": {
    "targetNames": [
      "A",
      "B",
      "C"
    ],
    "targetBases": [
      100,
      200,
      100
    ],
    "coveredBases": [
      0,
      50,
      0
    ]
  },
  "output": {
    "missingTargets": [
      "A",
      "C"
    ],
    "missingTargetBases": 200,
    "missingTargetCount": 2
  }
}

Limitations and assumptions

This uses supplied per-target summaries, not reads or interval alignments. Partially uncovered targets are not included.

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 On Target Read Efficiency for this operation: Compute capture efficiency as the fraction of mapped reads overlapping targets.

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

References

Zero Coverage Targets — tool.io

Similar or alternative tools

Callable Depth Fraction
Calculate callable-base percentage from a depth histogram and minimum calling depth.
On Target Read Efficiency
Compute capture efficiency as the fraction of mapped reads overlapping targets.