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The following tools are part of the [[BamUtil|BamUtil program]] which is built using [[C++ Library: libStatGen|libStatGen]].
The [[BamUtil|BamUtil program]] is built using [[C++ Library: libStatGen|libStatGen]]. Running <code>bin/bam</code> with no parameters will print the usage information for the <code>bam</code> executable. Running <code>bin/bam ''subProgram''</code> will print the usage information for the BamUtil sub-program.
Running <code>bin/bam</code> with no parameters will print the Usage information for the <code>bam</code> executable. Running <code>bin/bam ''subProgram''</code> will print the usage information for the BamUtil sub-program.
'''Tools to Rewrite SAM/BAM Files: '''
'''Tools to Rewrite SAM/BAM Files: '''
* [[BamUtil: findCigars|findCigars]] - Output just the reads that contain any of the specified CIGAR operations.
* [[BamUtil: findCigars|findCigars]] - Output just the reads that contain any of the specified CIGAR operations.
* [[BamUtil: convert#BAM File Recovery | BAM Recovery]] - Recover corrupted BAM files
* [[BamUtil: convert#BAM File Recovery | BAM Recovery]] - Recover corrupted BAM files
'''Tools to Modify & write SAM/BAM Files: '''
'''Tools to Modify & write SAM/BAM Files: '''
* [[BamUtil: dedup|dedup]] - Mark or remove duplicates, can also perform recalibration
* [[BamUtil: dedup|dedup]] - Mark or remove duplicates, can also perform recalibration
* [[BamUtil: recab|recab]] - Recalibrate base qualities
* [[BamUtil: recab|recab]] - Recalibrate base qualities
'''Informational Tools:'''
'''Informational Tools:'''
* [[BamUtil: gapInfo|gapInfo]] - Print information on the gap between read pairs in a SAM/BAM File.
* [[BamUtil: gapInfo|gapInfo]] - Print information on the gap between read pairs in a SAM/BAM File.
'''Helper Tools to Print Information In Readable Format:'''
''Helper Tools to Print Information In Readable Format:'''
* [[BamUtil: dumpHeader|dumpHeader]] - Print the SAM/BAM Header to the screen
* [[BamUtil: dumpHeader|dumpHeader]] - Print the SAM/BAM Header to the screen
* [[BamUtil: dumpRefInfo|dumpRefInfo]] - Print SAM/BAM Reference Name Information from the header
* [[BamUtil: dumpRefInfo|dumpRefInfo]] - Print SAM/BAM Reference Name Information from the header
* [[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: explainFlags|explainFlags]] - Describe SAM/BAM flags
* [[BamUtil: explainFlags|explainFlags]] - Describe SAM/BAM flags
'''Additional Tools:'''
'''Additional Tools:'''
* [[BamUtil: bam2FastQ|bam2FastQ]] - Convert the specified BAM file to fastQs.
* [[BamUtil: bam2FastQ|bam2FastQ]] - Convert the specified BAM file to fastQs.
'''Dummy/Example Tools:'''
'''Dummy/Example Tools:'''
* [[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
'''ASP programs: <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>'''
'''ASP programs: <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>'''
* [[BamUtil: asp | asp]] - perform an asynchronous pileup producing an ASP file.
* [[BamUtil: asp | asp]] - perform an asynchronous pileup producing an ASP file.
* [[BamUtil: dumpAsp|dumpAsp]] - perform an asynchronous pileup producing an ASP file.
* [[BamUtil: dumpAsp|dumpAsp]] - perform an asynchronous pileup producing an ASP file.
