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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.
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.
Originalsprog | Engelsk |
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Titel | WCGALP 2022 Programme book |
Antal sider | 4 |
Forlag | Wageningen Academic Publishers |
Publikationsdato | jul. 2022 |
Status | Udgivet - jul. 2022 |
Begivenhed | World Congress on Genetics Applied to Livestock Production - Rotterdam, Holland Varighed: 3 jul. 2022 → 8 jul. 2022 Konferencens nummer: 12 https://wcgalp.com/ |
Konference
Konference | World Congress on Genetics Applied to Livestock Production |
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Nummer | 12 |
Land/Område | Holland |
By | Rotterdam |
Periode | 03/07/2022 → 08/07/2022 |
Internetadresse |
Projekter
- 1 Afsluttet
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DairyCross: Krydsning - optimering på tværs af malkeracer
Thomasen, J. R. (PI), Nielsen, H. M. (Projektleder), Hjortø, L. (Deltager) & Kargo, M. (Deltager)
01/08/2018 → 30/09/2023
Projekter: Projekt › Forskning