I have SNP data for nuclear families with at least three children where one child has a disease and the siblings are 'normal'. Using these families, I was able to infer meiotic recombination events in the children. Subsequently, I binned these recombinations and isolated regions in the genome with an enrichment for recombination in cases compared to the sibling controls.
Using these regions, I want to explore the idea that recombinations can create novel haplotypes and so I wish to phase the SNPs in these bins.
I tried using plink but where a recombination occurs, plink fails to phase the region (returns NA). I am new to phasing and so would like to know what phasing software you would recommend and if it can handle recombinant regions.