AlphaImpute

AlphaImpute imputes and phases genotype data in pedigreed populations to support genomic evaluation and estimation of genomic breeding values by integrating genomic, phenotypic, and pedigree data.

Key Features:

• Genotype Imputation: Imputes alleles or allele probabilities for all animals in a pedigree, including completely ungenotyped individuals and those genotyped at low density, and can impute unmapped single nucleotide polymorphisms (SNPs).
• Phasing: Performs simple and long-range phasing to reconstruct haplotypes from genotype data.
• Haplotype Library Imputation: Utilizes a haplotype library to predict missing genotypes based on known haplotype structures.
• Segregation Analysis: Incorporates segregation analysis and Mendelian inheritance constraints within pedigrees to refine genotype predictions.
• Scalability and Efficiency: Designed to handle large datasets with computational costs feasible for pedigrees comprising up to 25,000 animals.
• Single-Stage Genomic Evaluation: Combines pedigree, genomic, and phenotypic information into a single-stage evaluation to increase the accuracy of estimated genomic breeding values.

Scientific Applications:

• Genomic Selection: Supports large-scale genomic selection by enabling the imputation and phasing required for genomic prediction and selection decisions.
• Breeding Programs: Applies to animal breeding programs by accommodating complex pedigree structures and low-density genotyping for precise genetic evaluations.
• Genetic Research: Facilitates studies of inheritance patterns, population genetics, and evolutionary biology to investigate genetic architecture.

Methodology:

Segregation analysis, haplotype library imputation, simple and long-range phasing, and integration of pedigree, genomic, and phenotypic data into a single-stage genomic evaluation.