Localized SNP Density

Find SNP-anchored half-open windows meeting a caller-defined localized density threshold.

Description

Localized SNP density counts nearby distinct positions within a genomic window.

Localized SNP density counts nearby distinct positions within a genomic window. Anchoring windows at observed SNPs avoids inventing a genomic scan grid.

Find SNP-anchored half-open windows meeting a caller-defined localized density threshold.

When to use Localized SNP Density

Use this for the following task: Find SNP-anchored half-open windows meeting a caller-defined localized density threshold.

Prepare the caller-filtered sequences, counts, coordinates or annotations requested below. Keep identifiers and paired lists aligned on the same reference.

How to use Localized SNP Density 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 snpPositions, windowBp, minimumSnps using the field table, then run the tool.
Read clusterStarts, clusterEnds, clusterCounts. 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
snpPositions	Zero-based SNP coordinates. Duplicates are counted once; each distinct SNP anchors a half-open window.	list of integer; minimum entries 1; maximum entries 100000; each entry: integer; minimum 0	Required
windowBp	Window bp	integer; minimum 1	Required
minimumSnps	Minimum snps	integer; minimum 1	Required

Deduplicate and sort nonnegative positions, then advance a right pointer for each left anchor. Return every qualifying window, including overlapping windows, with counts.^[1]

window = [SNPposition, SNPposition+windowBp); emit if distinct count ≥ minimum

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

Output field	Meaning	Value type
clusterStarts	Cluster starts	list of integer
clusterEnds	Cluster ends	list of integer
clusterCounts	Cluster counts	list of integer

json

{
  "input": {
    "snpPositions": [
      1,
      2,
      3,
      20
    ],
    "windowBp": 5,
    "minimumSnps": 3
  },
  "output": {
    "clusterStarts": [
      1
    ],
    "clusterEnds": [
      6
    ],
    "clusterCounts": [
      3
    ]
  }
}

Limitations and assumptions

Ends are excluded. The tool does not merge windows, account for callable territory or assign biological causes.

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 Indel Density for this operation: Compute insertion-plus-deletion variant density per callable kilobase. For a complementary task, use Structural Variant Size Bands for this operation: Classify structural variant sizes using caller-specified base-pair boundaries.

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

References

Localized SNP Density — tool.io

Similar or alternative tools

Indel Density
Compute insertion-plus-deletion variant density per callable kilobase.
Structural Variant Size Bands
Classify structural variant sizes using caller-specified base-pair boundaries.