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** [[BamUtil: splitChromosome|'''splitChromosome''' - Split BAM by Chromosome]]
** [[BamUtil: splitChromosome|'''splitChromosome''' - Split BAM by Chromosome]]
** [[BamUtil: writeRegion|'''writeRegion''' - Write the alignments in the indexed BAM file that fall into the specified region and/or have the specified read name]]
** [[BamUtil: writeRegion|'''writeRegion''' - Write the alignments in the indexed BAM file that fall into the specified region and/or have the specified read name]]
** [[BamUtil: findCigars|'''findCigars''' - Output just the reads that contain any of the specified CIGAR operations]]
** [[BamUtil: readIndexedBam|'''readIndexedBam''' - Read an indexed BAM file reference by reference id -1 to the max reference id and write it out as a SAM/BAM file]]
* Modify & write SAM/BAM Files
** [[BamUtil: filter|'''filter''' - Filter reads by clipping ends with too high of a mismatch percentage and by marking reads unmapped if the quality of mismatches is too high]]
** [[BamUtil: filter|'''filter''' - Filter reads by clipping ends with too high of a mismatch percentage and by marking reads unmapped if the quality of mismatches is too high]]
** [[BamUtil: revert|'''revert''' - Revert SAM/BAM replacing the specified fields with their previous values (if known) and removes specified tags]]
** [[BamUtil: revert|'''revert''' - Revert SAM/BAM replacing the specified fields with their previous values (if known) and removes specified tags]]
** [[BamUtil: squeeze|'''squeeze''' - reduces files size by dropping OQ fields, duplicates, specified tags, using '=' when a base matches the reference, binning quality scores, and replacing readNames with unique integers]]
** [[BamUtil: squeeze|'''squeeze''' - reduces files size by dropping OQ fields, duplicates, specified tags, using '=' when a base matches the reference, binning quality scores, and replacing readNames with unique integers]]
* Informational Tools
* Informational Tools
