Callable Depth Fraction
Calculate callable-base percentage from a depth histogram and minimum calling depth.
Description
A minimum-depth rule can summarize callable territory from a histogram.
A minimum-depth rule can summarize callable territory from a histogram. Depth is one calling criterion among several possible quality requirements.
Calculate callable-base percentage from a depth histogram and minimum calling depth.
When to use Callable Depth Fraction
Use this for the following task: Calculate callable-base percentage from a depth histogram and minimum calling 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 Callable Depth Fraction 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 depthValues, baseCounts, minimumDepth using the field table, then run the tool.
- Read callableBases, totalBases, callablePercent. 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 |
|---|---|---|---|
| depthValues | Depth values | 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 |
| minimumDepth | Minimum depth | integer; minimum 0 | Required |
Supply distinct supported depth bins with aligned counts. Require a positive safe total and sum the bins meeting the inclusive cutoff.1
callableBases = Σ counts for depth ≥ minimum; percent = 100 callable/total This summarizes the declared operation. Units, indexing, inclusivity and exceptional cases are explained in the surrounding text.
| Output field | Meaning | Value type |
|---|---|---|
| callableBases | Callable bases | integer |
| totalBases | Total bases | integer |
| callablePercent | Callable percent | number |
{
"input": {
"depthValues": [
0,
10,
20
],
"baseCounts": [
5,
10,
5
],
"minimumDepth": 10
},
"output": {
"callableBases": 15,
"totalBases": 20,
"callablePercent": 75
}
}Limitations and assumptions
The tool does not apply mapping/base-quality or other callability filters. Threshold zero can include zero-depth bins by its explicit rule.
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 Depth Band Uniformity for this operation: Measure the fraction of covered bases within a caller-defined band around mean depth. For a complementary task, use Zero Coverage Targets for this operation: Tally target intervals with zero covered bases from supplied per-target coverage summaries.
The implementation reference documents the exact calculation, supported input shapes and returned fields.
References
-
Callable Depth Fraction — tool.io
Similar or alternative tools
- Depth Band Uniformity
Measure the fraction of covered bases within a caller-defined band around mean depth.
- Zero Coverage Targets
Tally target intervals with zero covered bases from supplied per-target coverage summaries.