Paternal recombination rate and maternal linkage disequilibrium
(LD) are estimated for pairs of biallelic markers such as single nucleotide
polymorphisms (SNPs) from progeny genotypes and sire haplotypes. At least
one sire has to be double heterozygous at the investigated pairs of SNPs.
The implementation relies on paternal half-sib families. If maternal half-
sib families are used, the roles of sire/dam are swapped. Multiple families
can be considered.
Hampel, Teuscher, Gomez-Raya, Doschoris, Wittenburg (2018) "Estimation of
recombination rate and maternal linkage disequilibrium in half-sibs"