Sperm-typing of two C57BL/6JxCAST/EiJ mouse crosses

A cross between Mus musculus domesticus (strain C57BL/6J, hereafter called B6) and Mus musculus castaneus (strain CAST/EiJ, hereafter called CAST) resulted in a F1 hybrid (B6xCAST). Sperm DNA was collected from 2 individuals of this cross (named 'BxC_1' and 'BxC_2'). The extracted DNA from both biological replicates was then sonicated to produce fragments of a mean size of 350 bp.After collecting sperm DNA from the two individuals, we performed capture-based DNA sequencing using an assay targeting 1,018 recombination hotspots and 500 control loci (that do not correspond to known recombination hotspots but that display similar genomic characteristics in terms of GC-content, SNP density, sequence quality and TE content).For the efficiency of DNA capture (i.e. hybridisation-based targeted-DNA enrichment) to be identical in both haplotypes, two baits were designed for each of the 1,518 selected regions: one corresponding to the CAST haplotype and one to the B6 haplotype.All libraries were subjected to either only one ('A' libraries) or two ('B' libraries) rounds of DNA capture.Libraries were then sequenced by an Illumina device using a 250-bp paired-end protocol, except for 4 libraries (out of 18) which were sequenced as a pilot experiment using a 100-bp paired-end protocol.Reads were then mapped to both the GRCm38/mm10 version of the B6 genome (ftp://ftp-mouse.sanger.ac.uk/ref/) and the CAST/EiJ draft genome (ftp://ftp-mouse.sanger.ac.uk/REL-1509-Assembly/) using BWA-MEM with default parameters and marking shorter split hits as secondary.