The glass rod and tubes we use as base are all clear. Color comes from adding metals to the glass and heating them up to form crystals. Silver, chromium, cadmium, and rare earth elements are popular sources of color, and each can produce a wide variety of colors, depending on how the crystals grow and how the glass is heated to activate the crystal growth.
A cane is a length of glass that's had color applied to it. You heat the base material, hold it beneath the flame, heat the color, then paint the color on the base. Apply just a bit of pressure as you do this. I found that holding the color steady, and moving the base beneath it, worked best. Use a small flame if the color rod is thin (eg, a stringer).
We created swirl marbles by first creating a cane, hot sealing a punty to the end, heating the cane, twisting as you heat, then pulling the last punty off. Form a marble at the end, this time using the graphite marble shaping tool. The glass will have the twisted color strands from the cane and will be clear inside (from the base glass). Cold seal the end, flame put the original punty, finish shaping the marble, then remove the cold seal.
Canes with contrasting colors work well. It's okay to leave gaps in the color; these'll turn into clear glass. If you heat the cane overall the colors will melt into the cane. You want to do at least enough of this to fuse the glass together. Twisting is good but don't twist too much, else the colors will turn muddy. Eg, a 45 degree twist wrt the long axis of the rod will look nice, but an 80 degree twist will be too thin and won't look great.
The marble shaping tool is a graphite block with divots of various sizes and a handle at one end (eg, here). You do not just push the hot glass into a divot in order to make a hemisphere. This would produce a harsh crease in the marble and wouldn't help you smooth anything out. Instead, think of the divots simply as rings, or bottomless pits. The purpose is to run the ring around the surface of the marble; a perfectly round marble will touch the rim of the hole at all times everywhere. If the marble is eccentric, moving the rim around the marble (or rotating the marble around and about the rim) will smooth out the lumps. Time in the flame and rotating the entire piece for even heat and gravity treatment will smooth out the surface. Yes, this truly works! The graphite can withstand tremendous temperatures, so you can introduce the very hot glass to the tool. I found what worked well was to let the glass cool just to a medium red, down from a very hot glow, before placing it on the tool. Also, it worked best to rotate the punty (spinning the marble) as I lay the marble into the divot, with the punty horizontal, so as to avoid pushing the rim into the soft glass and creating a crease. Choose a divot that's at least one size smaller than the marble. You don't want the marble to fall inside the divot; the rim of the divot should do all the work.