Most roofs have several penetrations through them, including pipe flashings. In order to ensure the integrity of the roof system, such flashings must be handled carefully.
For vertically seamed roofs that have significant detail to their patterns, flexible base pipe flashings are available that are installed on top of the metal panel, configured as necessary to go over the corrugations in the roofing, and screwed and sealed into place. For most other roof systems, the use of aluminum or galvanized steel flashings with integral neoprene boots that surround the pipe is often preferred. Check with your roofing manufacturer to see what they recommend. However, when flashing around pipes, it is advisable to have several watertight seals on each pipe. First, the underlayment should be brought up around and sealed to the pipe. Next, working in a second layer of underlayment that goes around and is sealed to the pipe, extending up under the next highest layer of underlayment, is a wise idea. On horizontally-run metal roofs, this piece of underlayment could extend down and rest on top of the top lock of the next lower course of roofing. This way, any water that reaches the underlayment gets directed back out on top of the roofing. When using the standard aluminum or steel and neoprene pipe flashings, they should be under the roofing around the pipe and then extend out on top of the roofing beneath the pipe. The edges of the flashing, where they go underneath any roofing, should be bent up to prevent water form rolling sideways. The roofing should be cut as tight as possible around the pipe and then sealed. Make sure that the sealant is not expected to “span” across any wide gaps or chasms in between the metal pieces.