Tag SNP Capture Coverage

Audit union coverage of target SNPs from caller-provided selected-tag capture edges.

Description

Tag SNPs can capture a union of target SNPs through supplied linkage edges.

Tag SNPs can capture a union of target SNPs through supplied linkage edges. Union counting avoids counting a target twice when several selected tags capture it.

Audit union coverage of target SNPs from caller-provided selected-tag capture edges.

When to use Tag SNP Capture Coverage

Use this for the following task: Audit union coverage of target SNPs from caller-provided selected-tag capture edges.

Prepare the observed records or explicit model parameters requested below. Keep probabilities as fractions and paired records aligned.

How to use Tag SNP Capture Coverage and understand its results

Prepare the observed records or explicit model parameters requested below. Keep probabilities as fractions and paired records aligned.
Enter selectedTags, targetSnps, edgeTags, edgeTargets using the field table, then run the tool.
Read capturedSnps, uncapturedSnps, capturePercent. 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
selectedTags	Selected tags	list of string; each entry: string	Required
targetSnps	Target snps	list of string; each entry: string	Required
edgeTags	Edge tags	list of string; each entry: string	Required
edgeTargets	Edge targets	list of string; each entry: string	Required

Supply distinct nonempty targets and aligned valid edge tags/targets. Keep edges whose tag is selected, build their target union and preserve target order in captured/uncaptured lists.^[1]

capture% = 100 distinct captured targets/targetCount

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

Output field	Meaning	Value type
capturedSnps	Captured snps	list of string
uncapturedSnps	Uncaptured snps	list of string
capturePercent	Capture percent	number

json

{
  "input": {
    "selectedTags": [
      "T1"
    ],
    "targetSnps": [
      "A",
      "B",
      "C"
    ],
    "edgeTags": [
      "T1",
      "T1",
      "T2"
    ],
    "edgeTargets": [
      "A",
      "B",
      "C"
    ]
  },
  "output": {
    "capturedSnps": [
      "A",
      "B"
    ],
    "uncapturedSnps": [
      "C"
    ],
    "capturePercent": 66.66666666666667
  }
}

Limitations and assumptions

Linkage edges and thresholds are inputs. The tool does not estimate LD or optimize tag selection.

The tool evaluates supplied observations or a declared model. It does not establish the biological cause of an observed pattern. 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 Solid Spine Haplotype Block for this operation: Extend a solid-spine block from the first SNP while both boundary SNPs retain caller-required linkage with all enclosed SNPs. For a complementary task, use Signed Dprime for this operation: Normalize signed linkage disequilibrium D by its sign-specific feasible maximum.

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

References

Tag SNP Capture Coverage — tool.io

Similar or alternative tools

Solid Spine Haplotype Block
Extend a solid-spine block from the first SNP while both boundary SNPs retain caller-required linkage with all enclosed SNPs.
Signed Dprime
Normalize signed linkage disequilibrium D by its sign-specific feasible maximum.