tldr/pages/common/bedtools.md

# 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.
> Homepage: <https://bedtools.readthedocs.io/en/latest/>.

- 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`