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_madc_sanity       Run basic sanity checks on a MADC-style allele
                        report
check_ped               Check a pedigree file for accuracy and
                        report/correct common errors
check_replicates        Compatibility Between Samples Genotypes
dosage2vcf              Convert DArTag genotype reports and counts to
                        VCF
dosage_ratios           Calculate the Percentage of Each Dosage Value
filterMADC              Filter MADC Files
filterVCF               Filter a VCF file
find_parentage          Find Parentage Assignments for Progeny
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_multi          Convert MADC file to VCF using polyRAD for
                        multiallelic genotyping
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
validate_pedigree       Validate Pedigree Trios Using Mendelian Error
                        Analysis
