Question: are jace and clary really brother and sister in the books

Answer: No, Clary learns that Valentine Morgenstern, the main antagonist of the series, is her biological father and her mother's ex-husband. At the end of City of Bones, Valentine tells them that Clary and Jace are siblings -- which, they discover later in the series, is a lie. In the second book of the series, City of Ashes, Clary dates her best friend Simon, who has for a long time had a crush on her, in order to forget Jace during the torturous time of believing him to be her brother. She is told by the Seelie Queen that she has the ability to create runes that don't exist; but they do exist, which later enables her to destroy Valentine's ship using the ``Open'' rune. In the end of the second novel, Clary finds that an old friend of her mother, Madeleine, knows how to wake her mother, who has been in a magical coma since the first book.