bamutils

DNA-seq
	basecall	Base/variant caller
	minorallele	Find potential minor allele frequency (experimental)
RNA-seq
	cims	Finds regions of unusual deletions (CLIP-seq) (experimental)
	count	Calculates counts/FPKM for genes/BED regions/repeats (also CNV)
General
	best	Filter out multiple mappings for a read, selecting only the best
	convertregion	Converts region mapping to genomic mapping
	export	Export reads, mapped positions, and other tags
	expressed	Finds regions expressed in a BAM file
	extract	Extracts reads based on regions in a BED file
	filter	Removes reads from a BAM file based on criteria
	innerdist	Calculate the inner mate-pair distance from two BAM files
	junctioncount	Counts the number of reads spanning individual junctions.
	keepbest	Parses BAM file and keeps the best mapping for reads that have multiple mappings
	merge	Combine multiple BAM files together (taking best-matches)
	nearest	Find the nearest annotated BED region for each read (experimental)
	pair	Given two separately mapped paired files, re-pair the files
	pcrdup	Find and mark PCR duplicates (experimental)
	peakheight	Find the size (max height, width) of given peaks (BED) in a BAM file
	removeclipping	Postprocesses a BAM file to remove all clipping from reads and alignments (experimental)
	renamepair	Postprocesses a BAM file to rename pairs that have an extra /N value
	split	Splits a BAM file into smaller pieces
	stats	Calculates simple stats for a BAM file
	tag	Update read names with a suffix (for merging)
Conversion
	tobed	Convert BAM reads to BED regions
	tobedgraph	Convert BAM coverage to bedGraph (for visualization)
	tofasta	Convert BAM reads to FASTA sequences
	tofastq	Convert BAM reads back to FASTQ sequences
Misc
	check	Checks a BAM file for corruption
	cleancigar	Fixes BAM files where the CIGAR alignment has a zero length element