Lead SNP Region Windows

Build chromosome-clipped zero-based half-open lead-SNP windows including both radius boundaries.

Description

A lead-SNP window includes positions on both sides of a selected base.

A lead-SNP window includes positions on both sides of a selected base. Half-open representation requires adding one to the inclusive upper boundary.

Build chromosome-clipped zero-based half-open lead-SNP windows including both radius boundaries.

When to use Lead SNP Region Windows

Use this for the following task: Build chromosome-clipped zero-based half-open lead-SNP windows including both radius boundaries.

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

How to use Lead SNP Region Windows and understand its results

Prepare the observed records or explicit model parameters requested below. Keep probabilities as fractions and paired records aligned.
Enter leadPositionsBp, halfWindowBp, chromosomeLengthBp using the field table, then run the tool.
Read windowStarts, windowEnds. 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
leadPositionsBp	Zero-based chromosome positions; output windows are half-open.	list of number; each entry: number	Required
halfWindowBp	Half window bp	integer	Required
chromosomeLengthBp	Chromosome length bp	integer	Required

Use zero-based lead positions inside a positive chromosome length and a nonnegative integer radius. Clip windows to chromosome boundaries and preserve input order.^[1]

start=max(0,lead−radius); end=min(chromosomeLength,lead+radius+1)

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

Output field	Meaning	Value type
windowStarts	Window starts	list of number
windowEnds	Window ends	list of number

json

{
  "input": {
    "leadPositionsBp": [
      1000,
      2000
    ],
    "halfWindowBp": 100,
    "chromosomeLengthBp": 3000
  },
  "output": {
    "windowStarts": [
      900,
      1900
    ],
    "windowEnds": [
      1101,
      2101
    ]
  }
}

Limitations and assumptions

Radius zero returns the lead base’s one-base interval. No windows are merged or association significance assessed.

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 Localized SNP Density for this operation: Find SNP-anchored half-open windows meeting a caller-defined localized density threshold. For a complementary task, use BED Intersection for this operation: Intersect two chromosome-aware zero-based half-open BED intervals.

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

References

Lead SNP Region Windows — tool.io

Similar or alternative tools

Localized SNP Density
Find SNP-anchored half-open windows meeting a caller-defined localized density threshold.
BED Intersection
Intersect two chromosome-aware zero-based half-open BED intervals.