I have around 50 genotypes of a pant species with two parents.I would like to perform a SNP genotyping analysis. I have a few questions in this regard.
1. For SNP calling from essentially a draft genome (apple) and to observe variation from both the parents, would I need to co-assemble them or assemble them separately and call SNPs individually for both of them?
2. How would I be able to annotate these supposed SNPs with the lack of a proper reference (in house created draft genome)?