I used a jig with a small cutting wheel to score the bottle then heat the score line with boiling ( or near boiling for thinner glass) and then dip it in water to break along the line. Polish with emery cloth or high grit sandpaper. The less delta T between the hot water and the dip water the smoother the cut. Finding your preferred Temps for the thickness of the glass is the art.

Edit: Boiling water