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bedtools

A swiss-army knife of tools for genomic-analysis tasks. tldr-pages

On several platforms

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from tldr-pages, CC BY 4.0

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 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_fileIdentify

Intersect two files with a left outer join, 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_fileIdentify

Use a more efficient algorithm to intersect two pre-sorted files

bedtools intersect -a path/to/file1 -b path/to/file2 -sorted >path/to/output_fileIdentify

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 sumIdentify

Convert bam-formatted input file to a bed-formatted one

bedtools bamtobed -i path/to/file.bam >path/to/file.bedIdentify

Find for all features in file1.bed the closest one in file2.bed and write their distance in an extra column (input files must be sorted)

bedtools closest -a path/to/file1.bed -b path/to/file2.bed -dIdentify