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.

Install

All systems
curl cmd.cat/bedtools.sh
Debian Debian
apt-get install BEDTools
Ubuntu
apt-get install BEDTools
image/svg+xml Kali Linux
apt-get install BEDTools
Fedora
dnf install BEDTools
OS X
brew install BEDTools
Raspbian
apt-get install 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.

  • Intersect two files with respect to the sequences' strand and save the result to {{path/to/output_file}}:
    bedtools intersect -a path/to/file_1 -b path/to/file_2 -s > path/to/output_file
  • Intersect two files with a left outer join, i.e. report each feature from {{file_1}} and NULL if no overlap with {{file_2}}:
    bedtools intersect -a path/to/file_1 -b path/to/file_2 -lof > path/to/output_file
  • Using more efficient algorithm to intersect two pre-sorted files:
    bedtools intersect -a path/to/file_1 -b path/to/file_2 -sorted > path/to/output_file
  • Group file {{path/to/file}} based on the first three and the fifth column and summarize the sixth column by summing it up:
    bedtools groupby -i path/to/file -c 1-3,5 -g 6 -o sum
  • Convert bam-formated file to a bed-formated one:
    bedtools bamtobed -i path/to/file.bam > path/to/file.bed
  • Find for all features in {{file_1}}.bed the closest one in {{file_2}}.bed and write their distance in an extra column (input files must be sorted):
    bedtools closest -a path/to/file_1.bed -b path/to/file_2.bed -d

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