Different types of flashing are available. Some professionals prefer lead flashing for its durability. A properly sized lead boot slips over the roof vent and because it is malleable, it can be crimped over the top of the pipe to seal out water. The other alternative is flashing made from a rubber seal attached to an aluminum base, which some professionals prefer because it is inexpensive and the same piece can fit a wide variety of pipe sizes.
To select the proper flashing for your vents, you need accurate measurements of the pipes. Waste pipes are always measured by their inside, so measure the inside diameter and purchase a flashing boot that fits that size. The most common rubber and aluminum boots fit pipes between 1 1/2 and 3 inches, although other sizes are available if you need to accommodate larger pipes.
If you are replacing old flashing, but not necessarily the entire roof, be careful not to damage existing shingles, because it can be difficult to find replacement shingles that are the same color. Vent boots typically are held in place by six nails: two below the pipe, two in the middle and two above the pipe. Carefully pry up just enough shingles to expose the nails and remove them. Pull the flashing up, turning it 90 degrees so it slips out from underneath the shingles.
Proper installation methods call for roofing membrane to be installed to cover the hole through which the vent protrudes, then the flashing, then shingles. To install the membrane, cut a hole in it equal to the diameter of the pipe, and slide it over the pipe. Apply silicone around the pipe where it protrudes through the membrane, then fit the flashing boot over the pipe and nail it into place.
When shingles already are in place, you need to rotate the flashing 90 degrees as you slide it over the pipe to slide it under the shingles. When you removed the shingles to install the new flashing, you will have disturbed the asphalt adhesive that helped hold them in place. Run a bead of silicone above that strip of the adhesive strip. This holds the shingles in place until the asphalt can bond with the shingle. Apply extra silicone to the aluminum flashing where it comes in contact with the shingles.