I have SNP data from two parents and two offspring in a plant. I want to detect breakpoints/crossing over events using this data. Are there any publicly available tools to do that. I have seen in one of the bio-stars post which talks about tools which do recombination breakpoints analysis using tools like Hyphy as shown in Recombination breakpoint detection using information like LD etc. But I don't think that this is what I want.
Moreover I don't have raw sequence data or BAM files (and thus can't use Breakpointer https://github.com/ruping/Breakpointer) I only have the SNPs and chromsome positions for each genotype parents and offsprings and I want to detect the regions where the genetic material might be coming from one parent than other. I am sure some tools exist and I tried searching it on pubmed & google but may be with the wrong terminology. Breakpointer is the closest that I I want and I am sure there would be others as well I would appreciate if you can suggest some tools that would suit my task the best.
