Using DOF1 cross type for CCRIX x B6

[Dan Skelly]

Hi,

I am hoping to use qtl2 for a mapping design where we have a CCRIX/CCF1 line crossed to C57BL/6 (one might call this CCF1N1). 

From my reading of the documentation, it seems that the DOF1 cross type may work for this situation. I can easily provide the parental genotype data including 9 parents: the 8 CC/DO founders and then the 9th just repeating B6. However, is there a sensible way to specify the number of generations for this case where the parent is CCRIX rather than DO?

Is there another approach that might be more appropriate?

Thank you!

Dan

[Karl Broman]

That seems reasonable to me. I don't have any particular ideas about how to choose the number of generations, but it probably doesn't matter.

karl

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[Dan Skelly]

Great, thanks much for the advice!

Dan

[Karl Broman]

I just implemented an "hsf1" cross type,  like the "dof1" but assuming a more plain haplotype probabilities. This might be a better fit for your situation, say with like 8 generations.  It's sitting in an "hsf1" branch on github:

    install.packages("remotes")    

    remotes::install_github("kbroman/qtl2@hsf1")

karl