AlphaFamImpute

AlphaFamImpute performs genotype calling, phasing, and imputation in large full-sib families from SNP arrays and genotype-by-sequencing (GBS) data in diploid plants and animals.

Key Features:

• Two-step imputation: A structured approach that separates parental genotype inference and offspring imputation into sequential steps.
• Parental genotype phasing and imputation: Deduces parental genotypes by analyzing segregation states observed in offspring.
• Offspring genotype phasing and imputation: Phases and imputes offspring genotypes by identifying specific parental haplotype segments inherited by each offspring.
• Support for SNP arrays and GBS: Operates on genotype data derived from SNP arrays and genotype-by-sequencing (GBS) methodologies.
• Low-coverage GBS handling: Addresses missing and incorrect genotype calls arising from low-coverage GBS, including scenarios with sequencing <1x coverage.
• Optimization for outbred full-sib families: Tailored to the genetic structure of outbred full-sib family designs.
• Accuracy demonstrated by simulations: Performance and high-accuracy genotype calls have been evaluated through extensive simulations.

Scientific Applications:

• Plant and animal breeding: Improves genotype data quality for breeding program analyses in diploid species.
• Genetic diversity studies: Facilitates assessment of genetic variation within and between populations using imputed genotypes.
• Functional genomics and association studies: Provides more complete genotype datasets to support genotype–phenotype association analyses.

Methodology:

Implements a two-step computational procedure that first deduces parental genotypes from offspring segregation states and then phases and imputes offspring genotypes by identifying inherited parental haplotype segments, with accuracy evaluated via simulations.