bedtools
Verified for current stable LTS
Bedtools Commands
Bedtools command syntax with verified terminal examples.
Commands
6 commands for Bedtools
bedtools Operations
Bedtools Command: Intersect Files Strand
bedtools intersect -a <path/to/file_A> -b <path/to/file_B1 path/to/file_B2 ...> -s > <path/to/output_file> bedtools Operations
Bedtools Command: Intersect Left Outer Join
bedtools intersect -a <path/to/file1> -b <path/to/file2> -loj > <path/to/output_file> bedtools Operations
Bedtools Command: Intersect Pre Sorted Files
bedtools intersect -a <path/to/file1> -b <path/to/file2> -sorted > <path/to/output_file> bedtools Operations
Bedtools Command: Group By Columns And Sum
bedtools groupby -i <path/to/file> -c 1-3,5 -g 6 -o sum bedtools Operations
Bedtools Command: Convert Bam To Bed
bedtools bamtobed -i <path/to/file.bam> > <path/to/file.bed> bedtools Operations
Bedtools Command: Find Closest Features
bedtools closest -a <path/to/file1.bed> -b <path/to/file2.bed> -d Suggest a Bedtools Command
Submit missing workflows, corrections, or verified alternatives for this tool.
FAQ
Coverage: Focused examples for common Bedtools workflows.
Verified version: current stable LTS.
Verification: Test commands in a disposable workspace and submit notes for edge cases.