-Sc argument not working as expected

[ornobalam]

Hi!

I would expect the following pieces of code to be equivalent:

A: -SI 0.01 1 0.001 -Sc 0 1 400 400 0

B: -SI 0.01 1 0.001 -SAA 400 -SaA 400

But A produces a frequency trajectory (across replicates) that starts rising right after t=0.01, while B only rises very recently. Am I understanding the -Sc option incorrectly?

To provide some more context, my goal is to simulate selection on standing variation but in a way that the previously neutral variation extends into the past and I can retrieve their frequencies. I thought I could do this by setting the selection coefficient to zero using -Sc before a certain time.

Thanks!
Ornob