Soft Clip Breakpoints
Generate zero-based reference-boundary hints from terminal soft clips and aligned CIGAR span.
Description
Terminal soft clips identify read sequence outside an aligned reference span.
Terminal soft clips identify read sequence outside an aligned reference span. Their alignment boundaries can supply breakpoint hints for investigation.1
Generate zero-based reference-boundary hints from terminal soft clips and aligned CIGAR span.
When to use Soft Clip Breakpoints
Use this for the following task: Generate zero-based reference-boundary hints from terminal soft clips and aligned CIGAR span.
Prepare the caller-filtered sequences, counts, coordinates or annotations requested below. Keep identifiers and paired lists aligned on the same reference.
How to use Soft Clip Breakpoints 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 cigar, alignmentStart, minimumClipLength using the field table, then run the tool.
- Read leftClipLength, rightClipLength, breakpointHints. 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 |
|---|---|---|---|
| cigar | CIGAR | string; minimum text length 2; maximum text length 1000000; pattern ^(?:[1-9][0-9]*[MIDNSHP=X])+(?![\s\S]) | Required |
| alignmentStart | Zero-based reference start; subtract one from a mapped SAM POS. | integer; minimum 0 | Required |
| minimumClipLength | Minimum clip length | integer; minimum 1 | Required |
Parse supported CIGAR operations, disregard hard clips when finding terminal soft clips, and require a reference-consuming alignment. Emit left/right boundaries when clips meet the minimum inclusively.2
right boundary = zero-based alignmentStart + Σ lengths of M,D,N,=,X This summarizes the declared operation. Units, indexing, inclusivity and exceptional cases are explained in the surrounding text.
| Output field | Meaning | Value type |
|---|---|---|
| leftClipLength | Left clip length | integer |
| rightClipLength | Right clip length | integer |
| breakpointHints | Breakpoint hints | list of integer |
{
"input": {
"cigar": "5S10M3S",
"alignmentStart": 100,
"minimumClipLength": 4
},
"output": {
"leftClipLength": 5,
"rightClipLength": 3,
"breakpointHints": [
100
]
}
}Limitations and assumptions
These are hints, not called structural variants. AlignmentStart is zero based, unlike SAM POS; mismapping and biological interpretation need separate review.
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 CIGAR Operation Summary for this operation: Summarize CIGAR operations and distinguish query-consuming and reference-consuming bases. For a complementary task, use CIGAR Junction Positions for this operation: Extract zero-based half-open reference skip junctions from CIGAR N operations.
Further background: Background specification: Soft Clip Breakpoints.
References
-
Background specification: Soft Clip Breakpoints — GA4GH / HTS specifications
-
Soft Clip Breakpoints — tool.io
Similar or alternative tools
- CIGAR Operation Summary
Summarize CIGAR operations and distinguish query-consuming and reference-consuming bases.
- CIGAR Junction Positions
Extract zero-based half-open reference skip junctions from CIGAR N operations.