basecallBase/variant caller
 minoralleleFind potential minor allele frequency (experimental)


 cimsFinds regions of unusual deletions (CLIP-seq) (experimental)
 countCalculates counts/FPKM for genes/BED regions/repeats (also CNV)


 bestFilter out multiple mappings for a read, selecting only the best
 convertregionConverts region mapping to genomic mapping
 exportExport reads, mapped positions, and other tags
 expressedFinds regions expressed in a BAM file
 extractExtracts reads based on regions in a BED file
 filterRemoves reads from a BAM file based on criteria
 innerdistCalculate the inner mate-pair distance from two BAM files
 junctioncountCounts the number of reads spanning individual junctions.
 keepbestParses BAM file and keeps the best mapping for reads that have multiple mappings
 mergeCombine multiple BAM files together (taking best-matches)
 nearestFind the nearest annotated BED region for each read (experimental)
 pairGiven two separately mapped paired files, re-pair the files
 pcrdupFind and mark PCR duplicates (experimental)
 peakheightFind the size (max height, width) of given peaks (BED) in a BAM file
 removeclippingPostprocesses a BAM file to remove all clipping from reads and alignments (experimental)
 renamepairPostprocesses a BAM file to rename pairs that have an extra /N value
 splitSplits a BAM file into smaller pieces
 statsCalculates simple stats for a BAM file
 tagUpdate read names with a suffix (for merging)


 tobedConvert BAM reads to BED regions
 tobedgraphConvert BAM coverage to bedGraph (for visualization)
 tofastaConvert BAM reads to FASTA sequences
 tofastqConvert BAM reads back to FASTQ sequences


 checkChecks a BAM file for corruption
 cleancigarFixes BAM files where the CIGAR alignment has a zero length element