BIGpopA - Pedigree Validation Genetic Composition of Diploids & Polyploids
Tools for pedigree quality control and genomic breed/line
composition estimation in diploid and polyploid breeding
populations. 'BIGpopA' provides functions to check and correct
common pedigree errors, assign parentage from SNP genotype data
using Mendelian error rates, validate parent-offspring trios,
and estimate genome-wide breed or line composition using
quadratic programming. Pedigree validation and parentage
assignment support any ploidy, using a polysomic Mendelian test
for even ploidy and a homozygosity-based check for odd ploidy.
Genotypes can be supplied as dosage tables, VCF files, or
'PLINK' .ped files. For more details about the included
'breedTools' functions, see Funkhouser et al. (2017)
<doi:10.2527/tas2016.0003>.
