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
-
apt-get install BEDTools
- Ubuntu
-
apt-get install BEDTools
- Kali Linux
-
apt-get install BEDTools
- Fedora
-
dnf install BEDTools
- OS X
-
brew install BEDTools
- Raspbian
-
apt-get install BEDTools
- Dockerfile
- dockerfile.run/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
© tl;dr; authors and contributors