Simulations in which every individual in the sample was simulated from the original ones

[eriqande]

Simulations in which every individual in the sample was simulated from the original ones

[eriqande]

I am going to tackle this now. It will just need a few little changes in

gscramble-paper-sims-and-analyses/R/bias-sim-funcs.R

and then we will copy bias-sim-script.R into a new one: bias-sim-script-all-new-indivs.R and run it on the cluster.

In fact, we don't even need to modify the sim_admixed() function in bias-sim-funcs.R. Rather we just need to call it
twice: once for the admixed individuals, and another time for the reference ones.

In fact, it is even easier. I will just let the Qs variable for these simulations in the Snakefile be "1_sim_the_knowns" and then
we can use that to modify the behavior of bias-sim-script.R.

It looks like the results from the first set of runs is still up on SEDNA, so this should be pretty easy to add. But I gooched it, so those will all get rerun anyway

[eriqande]

These simulations are now done.