Pedigree validation or parentage assignment?
pedigree validation, parentage assignment, Mendelian error, candidate parents, SNP genotype, pedigree quality control
Pedigree validation tests whether the parents already recorded for an individual are compatible with the SNP genotype data. Parentage assignment starts with one or both parents unknown and searches a supplied candidate-parent pool for the most compatible assignment.
The two analyses use related genetic evidence, but they answer different questions. A validation result addresses a recorded relationship. An assignment result compares the candidates that were provided to the analysis.
Start with the question
| If your question is… | The task is… | BIGpopA function |
|---|---|---|
| Is the pedigree table structurally consistent? | Pedigree checking and correction | check_ped() |
| Do the recorded parents fit the offspring genotype? | Pedigree validation | validate_pedigree() |
| Which supplied candidate parent or parent pair best fits the offspring genotype? | Parentage assignment | find_parentage() |
These steps are complementary. Structural pedigree checking does not use SNP genotypes. Validation and assignment do.
What does pedigree validation test?
BIGpopA compares each recorded parent-offspring trio with a genotype matrix coded as 0, 1, and 2. At a marker, an incompatibility occurs when the observed offspring genotype is not possible from the recorded parental genotypes under Mendelian transmission, as described in the official validate_pedigree() documentation.
For example, if both recorded parents have genotype 0 at a diploid marker, an offspring genotype of 2 is incompatible at that marker. BIGpopA summarizes incompatibilities across the non-missing markers tested for the trio.
The validation report can distinguish:
- a trio that passes the configured Mendelian-error threshold;
- a trio that fails that threshold;
- a trio with too few non-missing markers;
- an individual without genotype data; and
- records with missing parent information.
The status depends on the data and the function settings. The numerical defaults supplied by BIGpopA are software defaults, not universal biological recommendations.
What does parentage assignment test?
Parentage assignment does not begin by testing one recorded pair. BIGpopA searches the candidate parents supplied to find_parentage() and reports the parent or pair with the lowest Mendelian-error or homozygous-mismatch rate for the selected method, as documented for find_parentage().
The available methods search for:
- the best male parent;
- the best female parent;
- the best parent without using a sex role; or
- the best male and female parent pair.
The result is conditional on the candidate pool. If a biological parent is absent from that pool, the analysis cannot select that parent. When multiple candidates tie, BIGpopA can report the tied solutions.
Why a mismatch is not a diagnosis by itself
A Mendelian incompatibility can be evidence that a recorded relationship is wrong, but genotype error and missing or poor-quality genotype data can also affect pedigree inference. Published pedigree-reconstruction work therefore treats marker quality, missingness, available relatives, and the analysis model as part of the interpretation rather than treating a single mismatch count as proof (Wang 2019; Huisman 2017).
BIGpopA reflects this distinction by reporting statuses such as low_markers, no_genotype_data, and high_error rather than forcing every record into a parentage conclusion.
Read the two results differently
Validation result
Read it as: Do the recorded parents fit the available marker evidence under these settings?
A failure identifies a recorded trio that needs review. It does not by itself identify why the conflict occurred.
Assignment result
Read it as: Which of the supplied candidates best fits the available marker evidence under these settings?
The selected candidate is the best result within the searched pool. Review ties, marker counts, and error status before changing a pedigree record.
Where structural checking fits
Run check_ped() before genotype-based validation when the pedigree may contain duplicate rows, conflicting parent records, inconsistent parent-sex roles, missing parent records, or cycles. The official check_ped() documentation lists the returned issue tables and corrected pedigree and specifies that cycles are reported for manual resolution.
This step prepares the pedigree structure. It does not determine whether the recorded biological relationships are supported by SNP data.
Practical takeaway
Use pedigree validation when the parents are recorded and you want to test those records. Use parentage assignment when a parent is unknown and you have a candidate pool to search. In either case, the available marker evidence and candidate set define what the analysis can evaluate.
Continue learning
Sources and further reading
- Chinchilla-Vargas J. 2026. BIGpopA Tutorial: Pedigree cleaning, validation, and parentage assignment from SNP genotype data. Material supplied for adaptation to Software Hub.
- Chinchilla-Vargas J, Sandercock A, University of Florida. 2026. BIGpopA: Pedigree Validation Genetic Composition of Diploids & Polyploids, version 1.0.5. Official source and function documentation
- Huisman J. 2017. Pedigree reconstruction from SNP data: parentage assignment, sibship clustering and beyond. Molecular Ecology Resources 17:1009-1024. doi:10.1111/1755-0998.12665
- Wang J. 2019. Pedigree reconstruction from poor quality genotype data. Heredity 122:719-728. doi:10.1038/s41437-018-0178-7