Insert Size QC

Summarize insert size using mean and sample standard deviation against explicit QC limits.

Description

Insert sizes describe paired-read fragment lengths.

Insert sizes describe paired-read fragment lengths. Their mean and sample variability can be compared with explicit library-quality expectations.

Summarize insert size using mean and sample standard deviation against explicit QC limits.

When to use Insert Size QC

Use this for the following task: Summarize insert size using mean and sample standard deviation against explicit QC limits.

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

How to use Insert Size QC 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 insertSizesBp, minimumMeanBp, maximumMeanBp, maximumSdBp using the field table, then run the tool.
Read meanInsertBp, sampleSdBp, withinQcLimits. 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
insertSizesBp	Insert sizes bp	list of integer; minimum entries 2; maximum entries 100000; each entry: integer; minimum 0	Required
minimumMeanBp	Minimum mean bp	number; minimum 0	Required
maximumMeanBp	Maximum mean bp	number; minimum 0	Required
maximumSdBp	Maximum sd bp	number; minimum 0	Required

Supply at least two supported sizes and ordered mean limits. Compute mean and sample SD with centered offsets, then apply inclusive mean and maximum-SD checks.^[1]

sample SD = sqrt(Σ(size−mean)^2/(n−1))

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

Output field	Meaning	Value type
meanInsertBp	Mean insert bp	number
sampleSdBp	Sample sd bp	number
withinQcLimits	Within qc limits	boolean

json

{
  "input": {
    "insertSizesBp": [
      100,
      200,
      300
    ],
    "minimumMeanBp": 150,
    "maximumMeanBp": 250,
    "maximumSdBp": 120
  },
  "output": {
    "meanInsertBp": 200,
    "sampleSdBp": 100,
    "withinQcLimits": true
  }
}

Limitations and assumptions

This does not infer insert sizes from alignments or detect multimodal structure. Limits must fit the library.

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 Read Pair Orientation for this operation: Classify mapped read strands on the same reference after ordering their distinct leftmost alignment starts. For a complementary task, use Depth Band Uniformity for this operation: Measure the fraction of covered bases within a caller-defined band around mean depth.

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

References

Insert Size QC — tool.io

Similar or alternative tools

Read Pair Orientation
Classify mapped read strands on the same reference after ordering their distinct leftmost alignment starts.
Depth Band Uniformity
Measure the fraction of covered bases within a caller-defined band around mean depth.