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81 bytes added, 15:00, 2 September 2011
Programs: bold the program names
* Rewrite SAM/BAM Files
** [[BamUtil: convert|'''convert ''' - Read a SAM/BAM file and write as a SAM/BAM file (optionally converts between '=' & bases in the sequence)]]** [[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: 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: 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: 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]]
* Informational Tools
** [[BamUtil: validate|'''validate|validate ''' - Read and Validate a SAM/BAM file]]** [[BamUtil: diff|'''diff ''' - Print the diffs between 2 bams]]** [[BamUtil: stats|'''stats ''' - Print the diffs between 2 bams]]
* Print Information in Readable Form:
** [[BamUtil: dumpHeader|'''dumpHeader ''' - Print SAM/BAM header]]** [[BamUtil: dumpRefInfo|'''dumpRefInfo ''' - Print SAM/BAM Reference Information]]** [[BamUtil: dumpIndex|'''dumpIndex ''' - Dump a BAM index file into an easy to read text version]]** [[BamUtil: readReference|'''readReference ''' - Print the reference string for the specified region]]

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