Young Adult fiction is distinguished from Adult fiction typically by the age of the protagonist(s) and the subject matter or experiences involved. You can, of course, have adult novels starring children (nobody would consider A Game of Thrones to be YA, even though most of the protagonists are children or teenagers), and there is some overlap (I've seen Ender's Game sitting on both shelves of the same store), but the two are generally pretty distinct.

I would prefer my novel not be classified as YA, for various reasons. My protagonist is a teenager, and while I intend to involve some adult themes I don't want them to feel forced or out of place. But ultimately, who makes that call?

Young adult vs adult fiction isn't about the age of the characters (though that usually does vary too), it's about the age of your readers.

If you're writing for adults, then write for adults and pitch your work that way to publishers, agents, and potential customers.

If you use a traditional publisher, they might want to classify your book as young adult, or not. And you can work that out directly with them.

Young adult fiction can have adult elements. Sex, violence, relationships, drugs, death, etc are all fair game. Ultimately though, it's about who you envision reading the book. This will change how you use those elements. A young adult novel is unlikely to have all of the elements or put them as in-your-face as, say, A Song of Ice and Fire does.

The difference is also about point of view. Through whose eyes are you seeing the events? Looking again at Game of Thrones (the first book in the series A Song of Ice and Fire), the child viewpoint chapters are very different from the adult viewpoint chapters. We the readers know it's a disturbing and dangerous world mostly because of the adult chapters. The kids are not exactly shielded from things (look at Bran's early chapters) but they don't see the big picture and they don't really understand what they do see.

You and your publisher will make this classification decision based on all these factors and others (like how the marketing winds are blowing). If a bookstore chooses a different classification, that's on them. You have no say. But the official classification generally holds (in libraries, in most stores, in online searches, etc).

Your publisher will decide where to file your book, and it's largely a marketing decision. In the USA, books are often shunted into YA if they can possibly fit there because it's a healthy market. Also schools will often pick up or promote YA books --even ones that are a bit edgy --because they're trying to get kids to read. (Also for this reason, it may be easier for you, the author, to sell your book to a publisher or agent as a YA project than as adult fiction.)

If you self-publish you'll probably make the decision yourself but you'll have the same market forces to wrestle with. However, schools usually won't pick up self-published books, so the calculations may be a bit different.

In general, books with YA main characters are almost always filed as YA unless they are clearly and flagrantly inappropriate for teenagers (and sometimes even if they are). This is often not a huge problem. Most young adults love reading books with adult themes, and there are plenty of adults who still read YA fiction (count me as one of them). Personally, I tend to find a lot of YA fiction to be better written, more interesting, and more deeply felt than most adult fiction. If you're at all on the fence about it, I would query it both as adult fiction and as YA, and see which one gets a better response.