Bedtools is a command-line tool. To bring up the help, just type bedtools

As you can see, there are multiple “subcommands” and for bedtools to work you must tell it which subcommand you want to use.

Examples:

• bedtools intersect
• bedtools merge
• bedtools subtract

What version am I using?:

• bedtools --version

How can I get more help?:

• bedtools --contact