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BIGpopA is an R package developed by Breeding Insight that provides tools for pedigree quality control and genomic breed/line composition estimation in diploid and polyploid breeding populations. It is designed to help researchers and breeders identify pedigree errors, assign parentage from SNP genotype data, and estimate genome-wide breed or line composition.
To install the latest CRAN version of BIGpopA:
install.packages("BIGpopA")
library(BIGpopA)To install the development version of BIGpopA, install from GitHub
using remotes:
install.packages("remotes")
remotes::install_github("Breeding-Insight/BIGpopA", dependencies = TRUE)
library(BIGpopA)| Function | Purpose |
|---|---|
check_ped() |
Detect and correct pedigree errors (duplicates, conflicting trios, missing parents, cycles, inconsistent sex roles) |
validate_pedigree() |
Validate parent-offspring trios against SNP genotypes using Mendelian error rates |
find_parentage() |
Assign the most likely parent(s) to progeny from candidate parents |
allele_freq_poly() |
Compute reference population allele frequencies |
solve_composition_poly() |
Estimate genome-wide breed/line composition by quadratic programming |
vcf_to_dosage() |
Convert a VCF (.vcf / .vcf.gz) to allele
dosages for any ploidy |
ped_to_dosage() |
Convert a PLINK .ped (with optional .map)
to allele dosages |
Pedigree validation and parentage assignment support any ploidy, using a polysomic Mendelian test for even ploidy and a homozygosity-based check for odd ploidy.
validate_pedigree(), find_parentage(),
allele_freq_poly() and
solve_composition_poly() accept genotypes in any of these
formats:
| Format | Notes |
|---|---|
Text file (.txt, .tsv,
.csv) |
ID column followed by marker columns coded as allele-B dosage (0, 1, …, ploidy) |
VCF (.vcf, .vcf.gz) or vcfR
object |
GT calls converted to ALT-allele dosage using the
function’s ploidy |
PLINK .ped (+ optional .map) |
Diploid only; the .map supplies marker names |
data.frame / data.table /
matrix |
Already-loaded dosage data |
# Same call, different input formats
find_parentage("genotypes.vcf.gz", "parents.txt", "progeny.txt", ploidy = 4)
find_parentage("genotypes.ped", "parents.txt", "progeny.txt")
# Breed/line composition from a reference and a validation VCF
freq <- allele_freq_poly("reference.vcf", populations, ploidy = 2)
comp <- solve_composition_poly("validation.vcf", freq, ploidy = 2)BIGpopA powers the pedigree and composition modules of Familia, a point-and-click interface for the same analyses.
BIGpopA development is supported by Breeding Insight, a USDA-funded initiative based at the University of Florida - IFAS.
If you use BIGpopA in your research, please cite as:
Chinchilla-Vargas, Josue, and Breeding Insight Team. 2026. “BIGpopA: Pedigree Validation and Breed/Line Composition Estimation for Diploid and Polyploid Species.” R package version 2.1.0. https://github.com/Breeding-Insight/BIGpopA.
These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.