WGBS Depth Filter

Filter WGBS cytosine sites by a caller-supplied coverage depth.

Description

Bisulfite-sequencing depth is an upstream coverage criterion for interpreting a locus.

Bisulfite-sequencing depth is an upstream coverage criterion for interpreting a locus.^[1]

Filter WGBS cytosine sites by a caller-supplied coverage depth.

When to use WGBS Depth Filter

Use this tool to filter WGBS cytosine sites by a caller-supplied coverage depth.

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 WGBS Depth 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 cytosineDepths, minimumDepth using the field table and calculation rules, then run the tool.
Read passingIndexes, failedIndexes, passingPercent. 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
cytosineDepths	Cytosine depths	list of number	Required
minimumDepth	Minimum depth	number	Required

Enter nonempty nonnegative integer depths and a nonnegative minimum. Return passing zero-based indices and percentage.

pass=depth≥minimum

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

Output field	Meaning	Value type
passingIndexes	Passing indexes	list of number
failedIndexes	Failed indexes	list of number
passingPercent	Passing percent	number

json

{
  "input": {
    "cytosineDepths": [
      5,
      10,
      20
    ],
    "minimumDepth": 10
  },
  "output": {
    "passingIndexes": [
      1,
      2
    ],
    "failedIndexes": [
      0
    ],
    "passingPercent": 66.66666666666666
  }
}

Limitations and assumptions

No alignment, methylation estimate or statistical precision is calculated.

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 Single-CpG Methylation: Calculate single-CpG methylation after background correction. For a complementary task, use RRBS Fragment Range: Filter RRBS fragment lengths against selected size bounds.

References

WGBS Depth Filter — tool.io

Similar or alternative tools

Single-CpG Methylation
Calculate single-CpG methylation after background correction.
RRBS Fragment Range
Filter RRBS fragment lengths against selected size bounds.