Calculation of Covariance Between Markers for Half-Sib Families R package hscovar version 0.4.2 The theoretical covariance between pairs of markers is calculated from either paternal haplotypes and maternal linkage disequilibrium (LD) or vise versa. A genetic map is required. Grouping of markers is based on the correlation matrix and a representative marker is suggested for each group. Employing the correlation matrix, optimal sample size can be derived for association studies based on a SNP-BLUP approach. The implementation relies on paternal half-sib families and biallelic markers. If maternal half-sib families are used, the roles of sire/dam are swapped. Multiple families can be considered. Wittenburg, Bonk, Doschoris, Reyer (2020) "Design of Experiments for Fine-Mapping Quantitative Trait Loci in Livestock Populations" <doi:10.1186/s12863-020-00871-1>. Carlson, Eberle, Rieder, Yi, Kruglyak, Nickerson (2004) "Selecting a maximally informative set of single-nucleotide polymorphisms for association analyses using linkage disequilibrium" <doi:10.1086/381000>. Software Depends: R (>= 3.5.0) Imports: parallel, Matrix, foreach, rlist, pwr Dörte Wittenburg <wittenburg@fbn-dummerstorf.de> Comprehensive R Archive Network (CRAN) Dörte Wittenburg [aut, cre], Michael Doschoris [aut], Jan Klosa [ctb] GPL (>= 2) 2021-04-13 application/tgz https://CRAN.R-project.org/package=hscovar doi:10.32614/CRAN.package.hscovar