Filename stem

The filename stem is an important concept in the usage of QTL Cartographer. Beginning with version 1.12, the QTL Cartographer programs utilize the filename stem ``qtlcart''. All files are then named using this stem and filename extensions relevant to the filetype. In the resource file example above, the ``-stem'' entry specifies ``corn'' as a stem for filenames. This means that when new files are created, they will have the stem ``corn'' followed by a logical extension. An example would be corn.map for a genetic linkage map. With some practice, you will know the contents of a file by its extension. You can set the filename stem on the command line with the -X option.