$ sudo apt-get remove bedtools 

Uninstall bedtools including dependent package

If you would like to remove bedtools and it's dependent packages which are no longer needed from Ubuntu,

$ sudo apt-get remove --auto-remove bedtools 

Use Purging bedtools

If you use with purge options to bedtools package all the configuration and dependent packages will be removed.

$ sudo apt-get purge bedtools 

If you use purge options along with auto remove, will be removed everything regarding the package, It's really useful when you want to reinstall again.

$ sudo apt-get purge --auto-remove bedtools 

See Also,