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Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations

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A comparison of different algorithms for phasing haplotypes using Holstein cattle genotypes and pedigree data.

Younes Miar¹, Mehdi Sargolzaei², Flavio S Schenkel³

¹Department of Animal Science and Aquaculture, Dalhousie University, Truro, Nova Scotia, Canada B2N 5E3; Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, Ontario, Canada N1G 2W1.

Journal of Dairy Science

|February 6, 2017

Summary

This study compared haplotype phasing algorithms in Holstein cattle. FImpute and Beagle demonstrated superior accuracy, with FImpute offering significant computational efficiency for large-scale genotype phasing.

Keywords:

haplotype inference imputation livestock phasing accuracy

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Area of Science:

Genetics
Bioinformatics
Computational Biology

Background:

Haplotype phasing is crucial for genetic studies, including disease research and population genetics.
Accurate phasing of genotypes to haplotypes is essential for downstream genetic analyses.

Purpose of the Study:

To evaluate and compare the performance of five popular haplotype phasing algorithms: Beagle, Findhap, FImpute, Impute2, and ShapeIt2.
To assess phasing accuracy and computational efficiency across various scenarios using different genotyping data densities and pedigree information.

Main Methods:

Phasing algorithms were tested on Holstein cattle genotype data (50k and 777k SNP density).
Six scenarios were evaluated: no parental information, sire-progeny pairs, and sire-dam-progeny trios, with and without pedigree data.
Performance metrics included phasing accuracy (%) and computational time (speed).

Main Results:

Beagle and FImpute consistently showed the highest phasing accuracy across all scenarios and data densities.
FImpute generally provided higher accuracy with parental genotype information available.
In the absence of parental data, Beagle and Impute2 (with adjusted parameters) were slightly more accurate than FImpute.
Findhap was the fastest algorithm, followed closely by FImpute, which was significantly faster than Beagle, ShapeIt2, and Impute2.

Conclusions:

FImpute and Beagle are the most accurate haplotype phasing algorithms for livestock populations.
FImpute's high accuracy combined with its computational efficiency makes it ideal for large-scale genotype phasing in cattle.
Algorithm choice depends on data availability (parental genotypes, pedigree) and computational resources.