There are different ways to say “where are you?” in Japanese. The best phrase to use will depend on the context or your choice. The simplest and most common way to say “where are you?” in the Japanese language is: あなたはどこですか？ (anata wa doko desu ka?). In this phrase, the characters are all hiragana. The majority of Japanese will ask the question in this particular way.
Nevertheless, this same phrase can be written entirely in kanji characters as 貴方は何処ですか。 Because the particular か is at the end of the phrase, the question mark will also be removed.
Otherwise, the same phrase can be restructured and written as: どこにいますか？ (Doko ni imasu ka?). Here, “you” has been removed from the question and, as such, the phrase can be roughly translated as: “where are at?” Although this may sound ambiguous, it is understandable in the Japanese language. It should be noted that lots of Japanese words can be used to mean “you”. So, you will likely come across many other phrases and sentences like this as your understanding of Japanese increases.