allele_freq_poly        Compute Allele Frequencies for Populations
calculate_Het           Calculate Observed Heterozygosity from a
                        Genotype Matrix
calculate_MAF           Calculate Minor Allele Frequency from a
                        Genotype Matrix
check_homozygous_trios
                        Check Homozygous Loci in Trios
check_ped               Evaluate Pedigree File for Accuracy
check_replicates        Compatibility Between Samples Genotypes
dosage2vcf              Convert DArTag Dosage and Counts to VCF
dosage_ratios           Calculate the Percentage of Each Dosage Value
filterMADC              Filter MADC Files
filterVCF               Filter a VCF file
flip_dosage             Switch Dosage Values from a Genotype Matrix
get_countsMADC          Obtain Read Counts from MADC File
imputation_concordance
                        Calculate Concordance between Imputed and
                        Reference Genotypes
madc2gmat               Convert MADC Files to an Additive Genomic
                        Relationship Matrix
madc2vcf_all            Converts MADC file to VCF recovering target and
                        off-target SNPs
madc2vcf_targets        Format MADC Target Loci Read Counts Into VCF
merge_MADCs             Merge MADC files
solve_composition_poly
                        Compute Genome-Wide Breed Composition
thinSNP                 Thin a dataframe of SNPs based on genomic
                        position
updog2vcf               Export Updog Results as VCF
