I would like to compare ~5 MB genomic (QTL) regions across two groups (resistant and susceptible) and identify variants that might majorly influence resistance. I was thinking of the following pipeline;
- use susceptible cultivar as the reference (since there is only one)
- Assemble tolerant groups (3 cultivars) using the above as a reference
- Call variants
Since I won't be using reads here, can you suggest the most appropriate tools I can use for the purpose? I wasn't sure whether it is appropriate to use a small reads assembly and variant calling pipeline for this purpose (esp since those ask to give seq. platform). I really appreciate any help you can provide.