bedtools

all

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.

Examples (6)

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