On Bait Enrichment
Estimate target enrichment relative to the genomic fraction covered by baits.
Description
Bait enrichment compares observed on-bait read fraction with the bait fraction of the genome.
Bait enrichment compares observed on-bait read fraction with the bait fraction of the genome. It expresses enrichment over a simple uniform genomic baseline.
Estimate target enrichment relative to the genomic fraction covered by baits.
When to use On Bait Enrichment
Use this for the following task: Estimate target enrichment relative to the genomic fraction covered by baits.
Prepare the caller-filtered sequences, counts, coordinates or annotations requested below. Keep identifiers and paired lists aligned on the same reference.
How to use On Bait Enrichment 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 onBaitReads, totalMappedReads, baitBases, genomeBases using the field table, then run the tool.
- Read observedOnBaitFraction, expectedGenomicFraction, enrichmentFold. 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 |
|---|---|---|---|
| onBaitReads | On bait reads | integer; minimum 0 | Required |
| totalMappedReads | Total mapped reads | integer; minimum 1 | Required |
| baitBases | Bait bases | integer; minimum 1 | Required |
| genomeBases | Genome bases | integer; minimum 1 | Required |
Require positive totals and bait bases, with on-bait reads and bait bases bounded by their respective totals. Return both fractions and their quotient.1
enrichment = (onBaitReads/mappedReads)/(baitBases/genomeBases) This summarizes the declared operation. Units, indexing, inclusivity and exceptional cases are explained in the surrounding text.
| Output field | Meaning | Value type |
|---|---|---|
| observedOnBaitFraction | Observed on bait fraction | number |
| expectedGenomicFraction | Expected genomic fraction | number |
| enrichmentFold | Observed on-bait read fraction divided by the genomic bait fraction; reads, rather than aligned base counts, are used. | number |
{
"input": {
"onBaitReads": 800,
"totalMappedReads": 1000,
"baitBases": 100,
"genomeBases": 1000
},
"output": {
"observedOnBaitFraction": 0.8,
"expectedGenomicFraction": 0.1,
"enrichmentFold": 8
}
}Limitations and assumptions
Bait territory must be measured consistently without unintended overlap double counting. Coverage uniformity and capture bias are not modeled.
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 On Target Read Efficiency for this operation: Compute capture efficiency as the fraction of mapped reads overlapping targets. For a complementary task, use Depth Band Uniformity for this operation: Measure the fraction of covered bases within a caller-defined band around mean depth.
The implementation reference documents the exact calculation, supported input shapes and returned fields.
References
-
On Bait Enrichment — tool.io
Similar or alternative tools
- On Target Read Efficiency
Compute capture efficiency as the fraction of mapped reads overlapping targets.
- Depth Band Uniformity
Measure the fraction of covered bases within a caller-defined band around mean depth.