My son is being investigated by CPS for sexual abuse of his sister. What are the steps that will take place? Could a warrant be issued soon?

This is almost certainly going to end in your son's arrest. Typically, the steps are these: The girl will be told to go in for what's called a SANE exam. She'll be told to set up what's called a forensic examination at the equivalent (depending where this is) of the Child Assessment Center. She'll be questioned in such a way that there is no question of sexual abuse. The CAC will contact law enforcement. A warrant for his arrest will issue. It won't matter a bit if they find no medical evidence to support the allegations. Do not, under any circumstances, have your son talk to the police, CPS, the CAC, or any other government crony. To protect him you need to hire an attorney. A thorough investigation into these allegations may reveal the truth behind them.  The burden the cops must have to arrest your son is Probable Cause. Much more than that (Beyond a Reasonable Doubt) is needed in order to convict him.