While subroutines such as COUNT REC estimate the total number of recombinants in an interval, other subroutines are useful for inferring double recombinants in an individual. We used GENEHUNTER's HAPLOTYPE option and MERLIN's version 0.9.12b [2] best option to inspect the inferred haplotypes in the core nuclear family of pedigree 10043. Individuals 10000432, 10000635, and 10000804 were genotyped as heterozygotes with the Illumina platform and as 2/2 homozygotes with the Affymetrix platform. Figure 2 shows the GENEHUNTER output of the core pedigree for SNP markers 175–185. All genotypes are from Illumina except the middle marker, where the genotypes from Affymetrix have been substituted for rs958883. GENEHUNTER and MERLIN gave identical inferences for this pedigree. Both identified 3 double recombinants in adjacent intervals-namely intervals 179–180 and 180–181. When the Illumina genotypes are used, no double recombinants are inferred by either GENEHUNTER or MERLIN. (NB: in both the raw and the cleaned Illumina data set, the mother's (10001581) genotype at rs958883 is recorded as 1/1 whereas in the raw and the cleaned Affymetrix data set, the mother's genotype at tsc0260848 is recorded
