Here's a little tutorial on how to do it in Adobe Animate https://www.adobe.com/creativecloud/video/discover/rotoscoping-animation.html

Depending on the quality of your live action footage, you might be able to do it with stable diffusion, an AI driven image generation algorithm. I know this is /r/learnanimation and I should be ushering you into doing it traditionally, but if you're going to be submitting to festivals, using a novel animation technique like AI generated art could help you get into more festivals. It's probably not going to save you much time doing it this way - getting what you want out of AI generated art still takes a lot of time and trial and error, but might be worth delving into.

Pretty much any application that will let you import video will work, which is pretty much every software I'm aware of. I don't think any would have particular advantages over others.

You might run into some performance issues, though. I know using video in Clip Studio will absolutely balloon render times when trying to play it back. If the live footage is relatively stationary (like, the camera doesn't move and there's nothing in the scene that would overlap the characters), then you could always take stills of each background, import that, animate your scene, and then composite it in another software.

Creating an animation short to submit to festivals and would like to use live footage as the bg. 
What programs or combination of programs is best for this?

Adobe after effects is what I keep hearing. 
But could/should I animate in something like, toon boom and then export to after effects? 
Or could this be done fully in either or program?

Best software to animate over live footage