Mitochondrial Read Filter

Filter mitochondrial reads using caller-supplied chromosome aliases.

Description

Mitochondrial-read filtering depends on the reference assembly’s chromosome aliases.

Mitochondrial-read filtering depends on the reference assembly’s chromosome aliases.^[1]

Filter mitochondrial reads using caller-supplied chromosome aliases.

When to use Mitochondrial Read Filter

Use this tool to filter mitochondrial reads using caller-supplied chromosome aliases.

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 Mitochondrial Read Filter 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 readChromosomes, mitochondrialAliases using the field table and calculation rules, then run the tool.
Read retainedChromosomes, excludedReadCount, excludedPercent. 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
readChromosomes	Read chromosome names	list of string	Required
mitochondrialAliases	Mitochondrial chromosome aliases	list of string	Required

Enter nonempty chromosome labels and aliases; comparison trims and lowercases. Return original retained strings, excluded count and percentage.

exclude when normalized chromosome is in normalized alias set

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

Output field	Meaning	Value type
retainedChromosomes	Retained read chromosomes	list of string
excludedReadCount	Excluded mitochondrial reads	integer; minimum: 0
excludedPercent	Excluded read share (%)	number; minimum: 0; maximum: 100

json

{
  "input": {
    "readChromosomes": [
      "chr1",
      "chrM",
      "MT",
      "chr2"
    ],
    "mitochondrialAliases": [
      "chrM",
      "MT"
    ]
  },
  "output": {
    "retainedChromosomes": [
      "chr1",
      "chr2"
    ],
    "excludedReadCount": 2,
    "excludedPercent": 50
  }
}

Limitations and assumptions

Aliases may be empty. No automatic MT/chrM equivalence or alignment is added.

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 Chromosome Name Normalizer: Normalize chromosome names to a caller-selected chr-prefix convention. For a complementary task, use Blacklist Overlap Filter: Exclude genomic intervals that overlap caller-supplied blacklist intervals.

References

Mitochondrial Read Filter — tool.io

Similar or alternative tools

Chromosome Name Normalizer
Normalize chromosome names to a caller-selected chr-prefix convention.
Blacklist Overlap Filter
Exclude genomic intervals that overlap caller-supplied blacklist intervals.