If you are contemplating building a custom home, there are many decisions you'll need to make along the way. One of the very first decisions, and arguably the most important, is who will actually be in charge of the construction. Hiring a professional custom home builder with a good reputation in your community is a good first step.
In my twenty-plus years of building custom homes, one thing I've noticed is that most people approach this in one of two ways. The first is by talking to several builders and getting bids, and the second is pre-selecting a builder based on reputation and recommendations from friends or associates.
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You should keep in mind that a completed house can be very different depending on who the actual builder is. Each builder will likely have a different standard for what quality of materials and work are acceptable, and as a result this often leads to very different completed homes.
A common misconception is that the local building department will be making periodic inspections that will ensure the home is being built properly. The fact is there are still many locations around the country that either don't have inspections at all or if they do inspections, they are not very thorough.
The bottom line is there is no building authority that will make any guarantees on a residential building under their jurisdiction; this is solely the responsibility of the builder or property owner.
If you feel confident in knowing which materials are appropriate and how they should be correctly installed, as well as what the minimum standard for quality of work should be, then basing your decision on price alone might work out for you.