Methylation Haplotype Tally
Tally methylation haplotypes across phased binary reads.
Description
Binary methylation haplotypes summarize per-read states across a specified CpG count.
Binary methylation haplotypes summarize per-read states across a specified CpG count.1
Tally methylation haplotypes across phased binary reads.
When to use Methylation Haplotype Tally
Use this tool to tally methylation haplotypes across phased binary reads.
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 Methylation Haplotype Tally 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 readHaplotypes, expectedCpgCount using the field table and calculation rules, then run the tool.
- Read haplotypes, counts, phasedReadCount. 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 |
|---|---|---|---|
| readHaplotypes | Read haplotypes | list of string | Required |
| expectedCpgCount | Expected cpg count | number | Required |
Enter 0/1 strings with length equal to expectedCpgCount; return first-seen patterns, counts and total. Empty reads are accepted.
count each exact binary string Units, indexing, boundary conditions and exceptional cases are defined in the calculation rules above.
| Output field | Meaning | Value type |
|---|---|---|
| haplotypes | Haplotypes | list of string |
| counts | Counts | list of number |
| phasedReadCount | Phased read count | number |
{
"input": {
"readHaplotypes": [
"01",
"11",
"01",
"00"
],
"expectedCpgCount": 2
},
"output": {
"haplotypes": [
"01",
"11",
"00"
],
"counts": [
2,
1,
1
],
"phasedReadCount": 4
}
}Limitations and assumptions
Expected count must be ≥1 but is not explicitly integer-constrained; fractional counts cannot match nonempty strings. No alignment/phasing is performed.
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 Allele–Methylation Coupling: Detect allele-specific methylation from phased read counts.
References
-
Methylation Haplotype Tally — tool.io
Similar or alternative tools
- Single-CpG Methylation
Calculate single-CpG methylation after background correction.
- Allele–Methylation Coupling
Detect allele-specific methylation from phased read counts.