To remove just bedtools package itself from Debian 9 (Stretch) execute on terminal:
sudo apt-get remove bedtools
Uninstall bedtools and it's dependent packages
To remove the bedtools package and any other dependant package which are no longer needed from Debian Stretch.
sudo apt-get remove --auto-remove bedtools
If you also want to delete configuration and/or data files of bedtools from Debian Stretch then this will work:
sudo apt-get purge bedtools
To delete configuration and/or data files of bedtools and it's dependencies from Debian Stretch then execute:
sudo apt-get purge --auto-remove bedtools
More information about apt-get remove
Advanced Package Tool, or APT, is a free software user interface that works with core libraries to handle the installation and removal of software on Debian, Ubuntu and other Linux distributions. APT simplifies the process of managing software on Unix-like computer systems by automating the retrieval, configuration and installation of software packages, either from precompiled files or by compiling source code.
apt-get is the command-line tool for handling packages, and may be considered the user's "back-end" to other tools using the APT library.
apt-get remove is identical to install except that packages are removed instead of installed. Note that removing a package leaves its configuration files on the system. If a plus sign is appended to the package name (with no intervening space), the identified package will be installed instead of removed.
How to remove bedtools package from Debian 9 (Stretch)