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bedtools — A swiss-army knife of tools for genomic-analysis tasks. Used to intersect, group, convert, and count

Submitted by: @import:tldr-pages·Mar 2, 2026·

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bedtoolscommandforclitoolsknifearmyswiss

Problem

How to use the bedtools command: A swiss-army knife of tools for genomic-analysis tasks. Used to intersect, group, convert, and count data in BAM, BED, GFF/GTF, VCF format. More information: <https://bedtools.readthedocs.io/en/latest/content/overview.html#summary-of-available-tools>.

Solution

bedtools — A swiss-army knife of tools for genomic-analysis tasks. Used to intersect, group, convert, and count data in BAM, BED, GFF/GTF, VCF format. More information: <https://bedtools.readthedocs.io/en/latest/content/overview.html#summary-of-available-tools>.

Intersect file [a] and file(s) [b] regarding the sequences' [s]trand and save the result to a specific file:

bedtools intersect -a {{path/to/file_A}} -b {{path/to/file_B1 path/to/file_B2 ...}} -s > {{path/to/output_file}}

Intersect two files with a [l]eft [o]uter [j]oin, i.e. report each feature from file1 and NULL if no overlap with file2:

bedtools intersect -a {{path/to/file1}} -b {{path/to/file2}} -loj > {{path/to/output_file}}

Using more efficient algorithm to intersect two pre-sorted files:

bedtools intersect -a {{path/to/file1}} -b {{path/to/file2}} -sorted > {{path/to/output_file}}

[g]roup a file based on the first three and the fifth [c]olumn and apply the sum [o]peration on the sixth column:

bedtools groupby -i {{path/to/file}} -c 1-3,5 -g 6 -o sum

Convert bam-formatted [i]nput file to a bed-formatted one:

bedtools bamtobed -i {{path/to/file.bam}} > {{path/to/file.bed}}

Find for all features in file1.bed the closest one in file2.bed and write their [d]istance in an extra column (input files must be sorted):

bedtools closest -a {{path/to/file1.bed}} -b {{path/to/file2.bed}} -d

Code Snippets

Intersect file [a] and file(s) [b] regarding the sequences' [s]trand and save the result to a specific file

bedtools intersect -a {{path/to/file_A}} -b {{path/to/file_B1 path/to/file_B2 ...}} -s > {{path/to/output_file}}

Intersect two files with a [l]eft [o]uter [j]oin, i.e. report each feature from `file1` and NULL if no overlap with `file2`

bedtools intersect -a {{path/to/file1}} -b {{path/to/file2}} -loj > {{path/to/output_file}}

Using more efficient algorithm to intersect two pre-sorted files

bedtools intersect -a {{path/to/file1}} -b {{path/to/file2}} -sorted > {{path/to/output_file}}

[g]roup a file based on the first three and the fifth [c]olumn and apply the sum [o]peration on the sixth column

bedtools groupby -i {{path/to/file}} -c 1-3,5 -g 6 -o sum

Convert bam-formatted [i]nput file to a bed-formatted one

bedtools bamtobed -i {{path/to/file.bam}} > {{path/to/file.bed}}

Context

tldr-pages: common/bedtools

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