Depth Band Uniformity
Measure the fraction of covered bases within a caller-defined band around mean depth.
Description
Coverage uniformity describes how much territory falls near the mean depth.
Coverage uniformity describes how much territory falls near the mean depth. Histogram base counts weight the average and the accepted band.
Measure the fraction of covered bases within a caller-defined band around mean depth.
When to use Depth Band Uniformity
Use this for the following task: Measure the fraction of covered bases within a caller-defined band around mean depth.
Prepare the caller-filtered sequences, counts, coordinates or annotations requested below. Keep identifiers and paired lists aligned on the same reference.
How to use Depth Band Uniformity 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 depths, baseCounts, minimumMeanFraction, maximumMeanFraction using the field table, then run the tool.
- Read meanDepth, withinBandBases, withinBandPercent. 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 |
|---|---|---|---|
| depths | Depths | list of integer; minimum entries 1; maximum entries 100000; each entry: integer; minimum 0 | Required |
| baseCounts | Base counts | list of integer; minimum entries 1; maximum entries 100000; each entry: integer; minimum 0 | Required |
| minimumMeanFraction | Minimum mean fraction | number; minimum 0 | Required |
| maximumMeanFraction | Maximum mean fraction | number; minimum 0 | Required |
Align supported depths/counts, require a positive safe total and positive mean, and count bases in the inclusive supplied mean-relative band.1
mean = Σdepth×baseCount/ΣbaseCount; band = [mean×minimumFraction, mean×maximumFraction] This summarizes the declared operation. Units, indexing, inclusivity and exceptional cases are explained in the surrounding text.
| Output field | Meaning | Value type |
|---|---|---|
| meanDepth | Mean depth | number |
| withinBandBases | Within band bases | integer |
| withinBandPercent | Within band percent | number |
{
"input": {
"depths": [
0,
10,
20
],
"baseCounts": [
1,
2,
1
],
"minimumMeanFraction": 0.5,
"maximumMeanFraction": 1.5
},
"output": {
"meanDepth": 10,
"withinBandBases": 2,
"withinBandPercent": 50
}
}Limitations and assumptions
The denominator is every supplied base count, including any zero-depth bin. This does not build a histogram or diagnose bias.
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 GC Coverage Dropout for this operation: Find GC bins with coverage deficits relative to a caller-supplied expected depth.
The implementation reference documents the exact calculation, supported input shapes and returned fields.
References
-
Depth Band Uniformity — tool.io
Similar or alternative tools
- Callable Depth Fraction
Calculate callable-base percentage from a depth histogram and minimum calling depth.
- GC Coverage Dropout
Find GC bins with coverage deficits relative to a caller-supplied expected depth.