no genetic map

[tanya-karagiannis]

I would like to use numbat for canine samples, but I do not have a genetic map to generate allele counts with pileup_and_phase.R. However, I do have the recombination rate (1 cM/Mb) and a phasing reference panel. Is it possible to generate the allele counts with cellsnp-lite first, and then incorporate the phasing and recombination rate information afterward? Do you have any suggestions for how to implement this?