A phasing algorithm targeted at dairy cattle populations having genotyped ancestors with many genotyped offspring

Morten Dahl*, Ole Fredslund Christensen

*Corresponding author af dette arbejde

Publikation: Bidrag til bog/antologi/rapport/proceedingKonferencebidrag i proceedingsForskningpeer review

Abstract

In dairy cattle, the prevalence of genomic testing is now widespread, and commonly both sires and many offspring in the form of children, grandchildren, and great-grandchildren, are genotyped. Calling phases from genotypes is useful for several reasons, in particular for construction of haplotypes and imputation of missing genotypes. In this paper, we present a new computationally efficient method to call phases of grandfathers and great-grandfathers when enough genotyped offspring are present. The method consists of first identifying shared
haplotypes between ancestor and offspring, followed by phasing segments based on homozygote genotypes in offspring, and finally merging haplotype segments to call entire ancestral haplotypes. The implementation is based on using bit vectors and fast binary computations. Results show that the method is effective in finding shared haplotypes to be used for phasing.
OriginalsprogEngelsk
TitelWCGALP 2022 Programme book
Antal sider4
ForlagWageningen Academic Publishers
Publikationsdatojul. 2022
StatusUdgivet - jul. 2022
BegivenhedWorld Congress on Genetics Applied to Livestock Production - Rotterdam, Holland
Varighed: 3 jul. 20228 jul. 2022
Konferencens nummer: 12
https://wcgalp.com/

Konference

KonferenceWorld Congress on Genetics Applied to Livestock Production
Nummer12
Land/OmrådeHolland
ByRotterdam
Periode03/07/202208/07/2022
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