Breakpoint Region Overlap

Map breakpoint positions to all overlapping supplied half-open regions; multiple annotations are retained rather than choosing one.

Description

Assign reported breakpoint positions to all overlapping caller-defined half-open genomic regions.

A breakpoint position is a reported coordinate associated with a structural change or a recombination analysis. Mapping it to a gene or annotation helps describe its location; an overlap alone does not establish the underlying event.

Regions use zero-based, half-open coordinates: start is included and end is excluded. A region [0, 20) contains positions 0 through 19, while position 20 may belong to a region starting at 20. Convert other coordinate conventions before comparing them.^[1]

The tool returns one assignment string per input breakpoint. When regions overlap, all matching names are joined with semicolons. A point outside every supplied region has an empty string, and unassignedCount counts those points.

When to use Breakpoint Region Overlap

Use it to annotate a prepared breakpoint list on a single coordinate axis, including overlapping functional regions that should all be reported.

How to use Breakpoint Region Overlap and interpret its calculation

Enter breakpointPositionsBp as nonnegative integer point coordinates; an empty list is allowed.
Enter aligned nonempty regionNames, regionStartsBp, and regionEndsBp lists. Each end must exceed its start.
Run the mapping, compare assignments with the original point order, and review empty assignments using unassignedCount.

point matches region when start ≤ position < end

Each matching region name is appended in region input order.

The implementation checks every point against every region without sorting either list. It preserves breakpoint order and joins all matches with semicolons; duplicates in names or positions are not deduplicated. To bound work, region count times the larger of one and breakpoint count cannot exceed one million.

json

{
  "input": {
    "breakpointPositionsBp": [
      10,
      20,
      30
    ],
    "regionNames": [
      "A",
      "B"
    ],
    "regionStartsBp": [
      0,
      20
    ],
    "regionEndsBp": [
      20,
      40
    ]
  },
  "output": {
    "assignments": [
      "A",
      "B",
      "B"
    ],
    "unassignedCount": 0
  }
}

An empty breakpoint list returns an empty assignments list and zero unassigned count. Names containing semicolons are not escaped, so use simple unambiguous labels if another program will split the output strings.

Limitations and assumptions

Coordinates must be nonnegative safe integers. There is no supplied genome length, so the tool cannot check whether regions or points fit the reference genome.

It performs point overlap rather than interval overlap, coordinate conversion, breakpoint calling, event validation, or phylogenetic inference. Caller-defined boundary coordinates must be translated to the intended point convention.

Alternative or Complementary methods

For deletion extent, merge intervals and count their union rather than assigning points. For retention of a specific functional interval, use a dedicated interval check with matching coordinates.

References

Genome Browser FAQ: BED format — UCSC Genome Browser

Similar or alternative tools

Defective Genome Deletion Union
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