Chromosome Name Normalizer

Normalize chromosome names to a caller-selected chr-prefix convention.

Description

Chromosome prefix conventions can be harmonized by an explicit string transformation.

Chromosome prefix conventions can be harmonized by an explicit string transformation.^[1]

Normalize chromosome names to a caller-selected chr-prefix convention.

When to use Chromosome Name Normalizer

Use this tool to normalize chromosome names to a caller-selected chr-prefix convention.

Prepare the already measured signals, counts, coordinates, fitted coefficients or sequence strings requested. Keep assay definitions, units, aligned lists and caller-selected thresholds consistent.

How to use Chromosome Name Normalizer and understand its results

Prepare the already measured signals, counts, coordinates, fitted coefficients or sequence strings requested. Keep assay definitions, units, aligned lists and caller-selected thresholds consistent.
Enter chromosomeNames, requireChrPrefix using the field table and calculation rules, then run the tool.
Read normalizedNames, changedCount, duplicateNames. The explanation below defines the units, signs, ordering and any flags or placeholder values.
If the tool reports an input issue, correct the values and run it again. Apply the stated assumptions when interpreting a successfully returned result.

Input field	Meaning	Value type; see rules below	Requirement
chromosomeNames	Chromosome names	list of string	Required
requireChrPrefix	Require chr prefix	boolean	Required

Enter string list/prefix option; return normalized labels, changed count and exact-case duplicates. Blank labels/empty list are accepted.

trim; remove one leading chr ignoring case; optionally prepend chr

Units, indexing, boundary conditions and exceptional cases are defined in the calculation rules above.

Output field	Meaning	Value type
normalizedNames	Normalized chromosome names	list of string
changedCount	Changed name count	integer; minimum: 0
duplicateNames	Duplicate normalized names	list of string

json

{
  "input": {
    "chromosomeNames": [
      "1",
      "chr2",
      "chrM"
    ],
    "requireChrPrefix": true
  },
  "output": {
    "normalizedNames": [
      "chr1",
      "chr2",
      "chrM"
    ],
    "changedCount": 1,
    "duplicateNames": []
  }
}

Limitations and assumptions

Suffix case and aliases remain; no assembly, validity or MT/M equivalence is resolved.

Numeric inputs, where present, must be finite. Follow the calculation-specific rules for overflow, underflow and exceptional cases. Lists are limited to 100,000 entries; the rules above may require smaller limits. Missing required fields, extra fields, wrong value types and violations of the calculation rules are input errors.

Alternative or Complementary methods

Use Mitochondrial Read Filter: Filter mitochondrial reads using caller-supplied chromosome aliases. For a complementary task, use Blacklist Overlap Filter: Exclude genomic intervals that overlap caller-supplied blacklist intervals.

References

Chromosome Name Normalizer — tool.io

Similar or alternative tools

Mitochondrial Read Filter
Filter mitochondrial reads using caller-supplied chromosome aliases.
Blacklist Overlap Filter
Exclude genomic intervals that overlap caller-supplied blacklist intervals.