*intersectBed (BAM)* Returns overlaps between two BED/GFF/VCF files.
*pairToBed (BAM)* Returns overlaps between a paired-end BED file and a regular BED/VCF/GFF file.
*bamToBed (BAM)* Converts BAM alignments to BED6, BED12, or BEDPE format.
*bedToBam (BAM)* Converts BED/GFF/VCF features to BAM format.
*bed12ToBed6* Converts "blocked" BED12 features to discrete BED6 features.
*bedToIgv* Creates IGV batch scripts for taking multiple snapshots from BED/GFF/VCF features.
*coverageBed (BAM)* Summarizes the depth and breadth of coverage of features in one BED versus features (e.g, "windows", exons, etc.) defined in another BED/GFF/VCF file.
*genomeCoverageBed (BAM)* Creates either a histogram, BEDGRAPH, or a "per base" report of genome coverage.
*unionBedGraphs* Combines multiple BedGraph files into a single file, allowing coverage/other comparisons between them.
*annotateBed* Annotates one BED/VCF/GFF file with overlaps from many others.
*groupBy* Summarizes data in a file/stream based on common columns.
*overlap* Returns the number of bases pairs of overlap b/w two features on the same line.
*pairToPair * Returns overlaps between two paired-end BED files.
*closestBed* Returns the closest feature to each entry in a BED/GFF/VCF file.
*subtractBed* Removes the portion of an interval that is overlapped by another feature.
*windowBed (BAM)* Returns overlaps between two BED/VCF/GFF files based on a user-defined window.
*mergeBed* Merges overlapping features into a single feature.
*complementBed* Returns all intervals _not_ spanned by the features in a BED/GFF/VCF file.
*fastaFromBed* Creates FASTA sequences based on intervals in a BED/GFF/VCF file.
*maskFastaFromBed* Masks a FASTA file based on BED coordinates.
*shuffleBed* Randomly permutes the locations of a BED file among a genome.
*slopBed* Adjusts each BED entry by a requested number of base pairs.
*sortBed* Sorts a BED file by chrom, then start position. Other ways as well.
*linksBed* Creates an HTML file of links to the UCSC or a custom browser.
