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.

Description

A solid-spine haplotype block requires both boundary SNPs to remain linked with enclosed SNPs.

A solid-spine haplotype block requires both boundary SNPs to remain linked with enclosed SNPs. This can differ from requiring strong linkage for every internal pair.

Extend a solid-spine block from the first SNP while both boundary SNPs retain caller-required linkage with all enclosed SNPs.

When to use Solid Spine Haplotype Block

Use this for the following task: Extend a solid-spine block from the first SNP while both boundary SNPs retain caller-required linkage with all enclosed SNPs.

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

How to use Solid Spine Haplotype Block and understand its results

Prepare the observed records or explicit model parameters requested below. Keep probabilities as fractions and paired records aligned.
Enter snpIds, dprimeMatrix, minimumAbsoluteDprime using the field table, then run the tool.
Read blockEndIndex, blockSnps. 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
snpIds	Snp ids	list of string; each entry: string	Required
dprimeMatrix	Dprime matrix	list of list of number; each entry: list of number; each entry: number	Required
minimumAbsoluteDprime	Minimum absolute dprime	number	Required

Supply at most 128 distinct ordered SNPs with a square signed D-prime matrix, symmetric within 1e−10. Starting at the first SNP, extend until the first failing endpoint and return the inclusive zero-based block end.^[1]

extend while |D′(first,j)| and |D′(candidateEnd,j)| ≥ cutoff for all relevant j

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

Output field	Meaning	Value type
blockEndIndex	Block end index	number
blockSnps	Block snps	list of string

json

{
  "input": {
    "snpIds": [
      "A",
      "B",
      "C"
    ],
    "dprimeMatrix": [
      [
        1,
        0.9,
        0.9
      ],
      [
        0.9,
        1,
        0.2
      ],
      [
        0.9,
        0.2,
        1
      ]
    ],
    "minimumAbsoluteDprime": 0.8
  },
  "output": {
    "blockEndIndex": 1,
    "blockSnps": [
      "A",
      "B"
    ]
  }
}

Limitations and assumptions

Only the block anchored at the first SNP is returned. The matrix and criterion are inputs; no full block partition is built.

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 Signed Dprime for this operation: Normalize signed linkage disequilibrium D by its sign-specific feasible maximum. For a complementary task, use Tag SNP Capture Coverage for this operation: Audit union coverage of target SNPs from caller-provided selected-tag capture edges.

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

References

Solid Spine Haplotype Block — tool.io

Similar or alternative tools

Signed Dprime
Normalize signed linkage disequilibrium D by its sign-specific feasible maximum.
Tag SNP Capture Coverage
Audit union coverage of target SNPs from caller-provided selected-tag capture edges.