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.

• Intersect file a and file(s) b regarding the sequences’ strand 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

• group a file based on the first three and the fifth column and apply the sum operation on the sixth column:

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

• Convert bam-formatted input 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