Breeding Insight Genomics Functions for Polyploid and Diploid Species
Compute Allele Frequencies for Populations
Calculate Observed Heterozygosity from a Genotype Matrix
Calculate Minor Allele Frequency from a Genotype Matrix
Check Homozygous Loci in Trios
Evaluate Pedigree File for Accuracy
Compatibility Between Samples Genotypes
Calculate the Percentage of Each Dosage Value
Convert DArTag Dosage and Counts to VCF
Filter MADC Files
Filter a VCF file
Switch Dosage Values from a Genotype Matrix
Obtain Read Counts from MADC File
Calculate Concordance between Imputed and Reference Genotypes
Convert MADC Files to an Additive Genomic Relationship Matrix
Converts MADC file to VCF recovering target and off-target SNPs
Format MADC Target Loci Read Counts Into VCF
Merge MADC files
Compute Genome-Wide Breed Composition
Thin a dataframe of SNPs based on genomic position
Export Updog Results as VCF
Functions developed within Breeding Insight to analyze diploid and polyploid breeding and genetic data. 'BIGr' provides the ability to filter variant call format (VCF) files, extract single nucleotide polymorphisms (SNPs) from diversity arrays technology missing allele discovery count (DArT MADC) files, and manipulate genotype data for both diploid and polyploid species. It also serves as the core dependency for the 'BIGapp' 'Shiny' app, which provides a user-friendly interface for performing routine genotype analysis tasks such as dosage calling, filtering, principal component analysis (PCA), genome-wide association studies (GWAS), and genomic prediction. For more details about the included 'breedTools' functions, see Funkhouser et al. (2017) <doi:10.2527/tas2016.0003>, and the 'updog' output format, see Gerard et al. (2018) <doi:10.1534/genetics.118.301468>.
Useful links