Novel Variant Fraction

Calculate variants absent from a supplied reference ID set; requires harmonized variant representation.

Description

Novelty relative to a database means absence from the supplied reference identifiers.

Novelty relative to a database means absence from the supplied reference identifiers. It depends on both database coverage and variant representation.

Calculate variants absent from a supplied reference ID set; requires harmonized variant representation.

When to use Novel Variant Fraction

Use this for the following task: Calculate variants absent from a supplied reference ID set; requires harmonized variant representation.

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

How to use Novel Variant Fraction 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 variantIds, databaseVariantIds using the field table, then run the tool.
Read novelVariantIds, novelPercent. 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; minimum entries 1; maximum entries 100000; each entry: string; minimum text length 1; maximum text length 1000000; pattern \S	Required
databaseVariantIds	Database variant ids	list of string; minimum entries 0; maximum entries 100000; each entry: string; minimum text length 1; maximum text length 1000000; pattern \S	Required

Require nonempty distinct called IDs. Build a reference-ID set and preserve called order for IDs absent from it.^[1]

novelPercent = 100 absentIDs/calledIDs

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

Output field	Meaning	Value type
novelVariantIds	Novel variant ids	list of string
novelPercent	Novel percent	number

json

{
  "input": {
    "variantIds": [
      "A",
      "B",
      "C"
    ],
    "databaseVariantIds": [
      "B"
    ]
  },
  "output": {
    "novelVariantIds": [
      "A",
      "C"
    ],
    "novelPercent": 66.66666666666667
  }
}

Limitations and assumptions

This does not query a database, normalize variants or infer pathogenicity. Genome build and identifier representation must already agree.

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 Private Singleton Tally for this operation: Identify alternate alleles seen exactly once in the target and absent from all other samples. For a complementary task, use VCF Record Audit for this operation: Audit VCF record field count and essential fields for the supplied number of samples.

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

References

Novel Variant Fraction — tool.io

Similar or alternative tools

Private Singleton Tally
Identify alternate alleles seen exactly once in the target and absent from all other samples.
VCF Record Audit
Audit VCF record field count and essential fields for the supplied number of samples.