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** [[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]]
** [[SplitBam|'''splitBam''' - Split SAM/BAM file by Read Group.
* Modify & write SAM/BAM Files
