Imputation Info Gate

Filter imputed variants by a caller-defined INFO-score floor.

Description

Imputation INFO scores summarize upstream imputation quality.

Imputation INFO scores summarize upstream imputation quality. A threshold gate retains variants under a caller-defined policy.

Filter imputed variants by a caller-defined INFO-score floor.

When to use Imputation Info Gate

Use this for the following task: Filter imputed variants by a caller-defined INFO-score floor.

Prepare the observed records or explicit model parameters requested below. Keep probabilities as fractions and paired records aligned.

How to use Imputation Info Gate and understand its results

Prepare the observed records or explicit model parameters requested below. Keep probabilities as fractions and paired records aligned.
Enter variantIds, infoScores, minimumInfoScore using the field table, then run the tool.
Read retainedVariants, rejectedVariants, retainedPercent. 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
variantIds	Variant ids	list of string; each entry: string	Required
infoScores	Info scores	list of number; each entry: number	Required
minimumInfoScore	Minimum info score	number	Required

Align variant IDs with scores in [0,1] and a minimum in [0,1]. Preserve order in retained/rejected lists and return retained percent.^[1]

retain when infoScore ≥ minimumInfoScore

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

Output field	Meaning	Value type
retainedVariants	Retained variants	list of string
rejectedVariants	Rejected variants	list of string
retainedPercent	Retained percent	number

json

{
  "input": {
    "variantIds": [
      "A",
      "B"
    ],
    "infoScores": [
      0.9,
      0.2
    ],
    "minimumInfoScore": 0.8
  },
  "output": {
    "retainedVariants": [
      "A"
    ],
    "rejectedVariants": [
      "B"
    ],
    "retainedPercent": 50
  }
}

Limitations and assumptions

The tool does not impute variants or establish a universal cutoff. Different INFO definitions should not be mixed.

The tool evaluates supplied observations or a declared model. It does not establish the biological cause of an observed pattern. 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 Population PC Outliers for this operation: Flag population-PC1 outliers relative to an explicitly supplied reference mean and standard deviation. For a complementary task, use MAPQ Filter Fraction for this operation: Filter SAM mapping qualities by threshold while treating MAPQ 255 as unavailable.

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

References

Imputation Info Gate — tool.io

Similar or alternative tools

Population PC Outliers
Flag population-PC1 outliers relative to an explicitly supplied reference mean and standard deviation.
MAPQ Filter Fraction
Filter SAM mapping qualities by threshold while treating MAPQ 255 as unavailable.