# 12345789 -filetype qtls.inp ^ ^ ^ space space space
The spaces are necessary, because the input is token based. The program will read the second token in the file as a long integer and use it as an identifier for the file. Thus, each file should have a unique identifier following the pound symbol.
The -filetype qtls.inp tells the QTL Cartographer programs that this is a qtls.inp formatted file.