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.

bedtools intersect -a path/to/file_A -b path/to/file_B1 path/to/file_B2 ... -s > path/to/output_file

bedtools intersect -a path/to/file1 -b path/to/file2 -loj > path/to/output_file

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

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

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

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