Combining marker catalogs generated by reference-based and de novo approach?!

[A D]

Hello,

I am revisiting a project from my postdoc 3 years later (it is as haunting as it sounds). I had run the reference-based and de novo stacks pipelines to generate two SNP catalogs and combined these sets to create a linkage map with Joinmap. Can anyone tell me why this might be a terrible idea?!

I would much appreciate the wisdom from this group as this is no longer my field...

Thank you!

[Catchen, Julian]

Hi,

 

How did you combine them together? Did you process them both independently and combine them within JoinMap, or did you combine them at some Stacks stage? I’m not sure the efficacy of doing this (assuming you did it at the JoinMap stage) since you would have lots of redundant markers. If I had a reference genome, I would only do a de novo analysis if the reference was low quality or incomplete. If your reference is decent, you could align the assembled de novo loci onto it to see how many of them overlap a marker you already generate directly from the reference analysis. Anyway, your strategy will depend on what you are trying to do with the genetic map.