*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.
*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.
*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.
