A nice fine tooth jigsaw will do the trick. Cuts like a charm.
Make sure to draw out your lines perfectly and stick masking tape along the edge where the cut will be so that the jigsaw does not mar or scratch the surface. A nice filing with a good flat file after that can take off the rough edges and or round 'em out just like the stock items.
An important detail to consider when selecting glass thickness: When you have a post sedan door with its solid window frame, you can get away with as thin as 1/8 thickness glass because it always rides on the rails of the frame. It is snugged into place once the window is all the way up (closed position) and barely shakes depending on how aggressive the lobe of the cam is. More like a quite quiver which I think is pretty cool. It will at sometimes need a little guiding hand to get it to seat up in the rail channel up top during the closing.
It will ride looser when it's down (opened) but not a bother at all.
3/8 thickness will be a little more forgiving and know its trajectory on the rails, but heavier.
Now, if you are permanently attaching the glass (no up or down operation) and with no regulators, then you can save a whole lot of weight and quiver a little less.