I am looking at ways to generate a linkage map from the GBS data. The data comes from the mapping population (F2), but parents are not genotyped. Although I can easily call the SNPs using either Stacks or TasselGBS, I have no clue how can I create a genetic map. Also, genomes for both the parents are available (scaffolds for one parent, chromosomes for the other). Can anybody give me some ideas about how to proceed?
Thanks very much for your time!