The Rootkit Hunter configuration file is stored at /etc/rkhunter.conf. This file is well documented and contain many of Rootkit Hunter's configuration options.
The following are all options currently set.
TMPDIR=/var/lib/rkhunter/tmp DBDIR=/var/lib/rkhunter/db SCRIPTDIR=/usr/share/rkhunter/scripts LOGFILE=/var/log/rkhunter.log USE_SYSLOG=authpriv.warning AUTO_X_DETECT=1 ENABLE_TESTS=all DISABLE_TESTS=suspscan hidden_procs deleted_files packet_cap_apps apps HASH_CMD=sha256sum SCRIPTWHITELIST=/bin/egrep SCRIPTWHITELIST=/bin/fgrep SCRIPTWHITELIST=/bin/which SCRIPTWHITELIST=/usr/bin/ldd #SCRIPTWHITELIST=/usr/bin/lwp-request SCRIPTWHITELIST=/usr/sbin/adduser #SCRIPTWHITELIST=/usr/sbin/prelink #SCRIPTWHITELIST=/usr/sbin/unhide.rb DISABLE_UNHIDE=1 INSTALLDIR=/usr