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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.
bedtools intersect -a {path/to/file_1} -b {path/to/file_2} -s > {path/to/output_file}
bedtools intersect -a {path/to/file_1} -b {path/to/file_2} -lof > {path/to/output_file}
bedtools intersect -a {path/to/file_1} -b {path/to/file_2} -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/file_1}.bed -b {path/to/file_2}.bed -d
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