BIGpopA
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>.
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