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*[[C++ Executable: bam#convert|Convert]] – Convert between SAM & BAM
*[[C++ Executable: bam#convert|Convert]] – Convert between SAM & BAM
*[[C++ Executable: bam#writeRegion|WriteRegion]] – Write only reads in the specified region
*[[C++ Executable: bam#writeRegion|WriteRegion]] – Write only reads in the specified region
*[[Pileup]] – Pileup every base or just bases in specified region and write VCF - <span style="color:#D2691E">Coming Soon</span>
*[[Pileup]] – Pileup every base or just bases in specified region and write VCF
*[[C++ Executable: bam#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
*[[C++ Executable: bam#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
==== Update the File ====
==== Update the File ====
