MSI Locus Instability
Quantify unstable microsatellite loci using supplied assay flags and threshold.
Description
Microsatellite instability summaries count loci flagged unstable by an assay.
Microsatellite instability summaries count loci flagged unstable by an assay. The fraction’s interpretation depends on the tested locus panel and threshold.
Quantify unstable microsatellite loci using supplied assay flags and threshold.
When to use MSI Locus Instability
Use this for the following task: Quantify unstable microsatellite loci using supplied assay flags and 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 MSI Locus Instability 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 instabilityFlags, minimumUnstableFraction using the field table, then run the tool.
- Read unstableLoci, testedLoci, unstablePercent, exceedsThreshold. 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 |
|---|---|---|---|
| instabilityFlags | Instability flags | list of integer; minimum entries 1; maximum entries 100000; each entry: integer; minimum 0; maximum 1 | Required |
| minimumUnstableFraction | Minimum unstable fraction | number; minimum 0; maximum 1 | Required |
Supply a nonempty supported list of numeric 0/1 assay flags and a minimum fraction in [0,1]. Sum flags and compare inclusively.1
unstablePercent = 100 Σflags/locusCount; threshold met when fraction ≥ minimum This summarizes the declared operation. Units, indexing, inclusivity and exceptional cases are explained in the surrounding text.
| Output field | Meaning | Value type |
|---|---|---|
| unstableLoci | Unstable loci | integer |
| testedLoci | Tested loci | integer |
| unstablePercent | Unstable percent | number |
| exceedsThreshold | True when the unstable fraction is at least the supplied threshold. | boolean |
{
"input": {
"instabilityFlags": [
1,
0,
1,
0
],
"minimumUnstableFraction": 0.3
},
"output": {
"unstableLoci": 2,
"testedLoci": 4,
"unstablePercent": 50,
"exceedsThreshold": true
}
}Limitations and assumptions
The field exceedsThreshold includes equality. This does not determine flags from sequence data or provide a clinical classification.
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 Genomic Scar Composite for this operation: Combine supplied LOH, telomeric imbalance, and large-transition counts with explicit weights; not a clinical HRD test. For a complementary task, use SSR Motif Class for this operation: Reduce an SSR motif to its primitive repeat unit and classify its base length.
The implementation reference documents the exact calculation, supported input shapes and returned fields.
References
-
MSI Locus Instability — tool.io
Similar or alternative tools
- Genomic Scar Composite
Combine supplied LOH, telomeric imbalance, and large-transition counts with explicit weights; not a clinical HRD test.
- SSR Motif Class
Reduce an SSR motif to its primitive repeat unit and classify its base length.