I am sure there are other ways but I use carbide glass drill bits. They are a bit pricey ( 10-20 dollars USD depending on the size at home depot), but they do a really good job and are designed to cut glass so you have less of a chance of cracking it. There are cheaper sets out there on Amazon but I have found you have to replace them much more frequently and they just don't hold up as well.
hope that helps!