+.SH CONFIGURATION FILE
+.P
+Any of the command-line options mentioned above can be specified in a
+configuration file instead. We look for a file named \(dq.htsnrc\(dq
+in the user's home directory; its syntax is given by examples in the
+htsnrc.example file (included with \fBhtsn\fR).
+.P
+If you are using the \fI\-\-run\-as\-user\fR option, that means that
+the configuration file will need to go in that user's home directory
+(and not, for example, root's).
+.P
+Options specified on the command-line override those in the
+configuration file.
+