A stack pipe is also known as a soil stack. It allows air to enter the toilet plumbing system to aid in the movement of the water and debris and to vent it. The soil stack runs inside the walls and through the roof of the home. There is a potential leak point in the location where the roof is cut to accommodate the stack pipe. Sealing around the stack pipe is important to mitigating the possibility of a roof leak.
Pry off metal flashing from around the stack pipe, if it is present, using a flat pry bar. Remove all the nails that were used to secure the flashing.
Cut away the shingles from the stack pipe base using a utility knife. Remove the shingles in a 6-inch square around the base of the stack pipe. Ensure that the base roof underneath is free of nails and pieces of shingling material.
Brush roofing tar onto the area around the soil stack that you just cleared. Brush the tar on the area liberally using an old paintbrush that you never want to use again. Smear the tar under the edges of the remaining shingles around the cleared area.
Install a rubber soil stack boot onto the stack and press it into the tar on the roof. Adjust the boot so that it sits flat against the roof. Brush tar over the base of the boot and onto the roof around it to ensure the area is properly sealed.