here is some background to my question in the title: I have two genome versions, a scaffolded and unscaffolded one; as luck has it, the annotated version is the unscaffolded one. I would like to update the coordinates in the GFF file to the scaffolded version. I wanted to use crossMap (http://crossmap.sourceforge.net) for this, but I need a chain file. I already have an AGP file describing how the scaffolds were generated. I am thus looking for a tool that would convert the AGP tile to a chain file. Does such a tool exist?