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*[[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
*[[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
*[[BamUtil: convert#BAM File Recovery | BAM Recovery]] - Recover corrupted BAM files
*[[BamUtil: convert#BAM File Recovery | BAM Recovery]] - Recover corrupted BAM files
*[[BamUtil: asp | ASP]] - perform an asynchronous pileup producing an ASP file. <span style="color:#D2691E">ASP is a new format that is currently in production, so this tool is not yet available for public release.</span>
==== Update the File ====
==== Update the File ====
*[[BamUtil: squeeze|Squeeze]] - Reduce 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]] - Reduce 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: clipOverlap|ClipOverlap]] - Clip overlapping read pairs so they do not overlap
*[[BamUtil: clipOverlap|ClipOverlap]] - Clip overlapping read pairs so they do not overlap
==== Helper Tools to Print Readable Information ====
==== Helper Tools to Print Readable Information ====
*[[BamUtil: dumpIndex|DumpIndex]] - Print the BAM Index to the screen in a readable format
*[[BamUtil: dumpIndex|DumpIndex]] - Print the BAM Index to the screen in a readable format
*[[BamUtil: readReference|ReadReference]] - Print the reference string for the specified region to the screen.
*[[BamUtil: readReference|ReadReference]] - Print the reference string for the specified region to the screen.
*[[BamUtil: dumpAsp|DumpAsp]] - perform an asynchronous pileup producing an ASP file. <span style="color:#D2691E">ASP is a new format that is currently in production, so this tool is not yet available for public release.</span>
