Either select the edge and adjust its source and target port coordinates (see section "Ports" in the properties view in yEd's lower right corner) or go to "File" -> "Preferences", tab "Display" and adjust option "Edge Path Clip".
With the first approach it is possible to specify different offsets for each edge. However, layout algorithms use the port coordinates for arranging edges as well. Therefore, running a layout algorithm will usually overwrite your manual settings.
The second approach affects all edges at once and is visualization only (i.e. it is not affected by layout algorithms in any way). However, for edges that are actually shorter than the specified value, you will no longer see an edge at all.