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

TY - GEN

T1 - A phasing algorithm targeted at dairy cattle populations having genotyped ancestors with many genotyped offspring

AU - Dahl, Morten

AU - Christensen, Ole Fredslund

N1 - Conference code: 12

PY - 2022/7

Y1 - 2022/7

N2 - 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 sharedhaplotypes 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.

AB - 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 sharedhaplotypes 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.

M3 - Article in proceedings

BT - WCGALP 2022 Programme book

PB - Wageningen Academic Publishers

T2 - World Congress on Genetics Applied to Livestock Production

Y2 - 3 July 2022 through 8 July 2022

ER -