Luke Anderson-Trocmé

Reviving the thread, are the CNC compatible files available anywhere?

Interesting point about the dead-ends, makes sense. And yes, agreed to keep this for a TODO. Either way, I might try to prune the pedigree myself and run the sims...

Thanks for reviving this thread @Darokrithia. I'm not sure how sex is tracked during the simulations, as far as I know it is included in the metadata, but not actually...

 Maybe obvious to most, but I found that drawing out the inheritance paths helped clarify things to me (edit: RED -- male probands potential inheritance, BLUE -- female probands...

Yes exactly. Sorry I should have clarified this from the top. This is in the context of fixed pedigree ancestry simulations. > On Aug 10, 2022, at 11:51 PM, Daniel...

```R # Get the deepest generation for each internal node maximum_genealogical_depth

I'll note here that I knew in advance that the French-Canadian genealogy was less than 18 generations hence the for loop, but this could be done with a while loop...

Thanks for the links to the code snippets, it looks like we already have everything we need to remove these regions. It seems like you're describing two possible options: **Option...

Pasting over Jeromes comments about the mask file from the email chain which is relevant here: > You're right about the strict mask, but unfortunately if we apply it to...

Let's go with plan A. I'll start writing it up to remove the centromeres. (It should be easy to include other intervals down the line) As for the repeat regions,...