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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.

Intersect two files regarding the sequences' strand and save the result to the specified 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-formatted file to a bed-formatted 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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