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, 15:04, 2 September 2011
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| ** [[BamUtil: splitChromosome|'''splitChromosome''' - Split BAM by Chromosome]] | | ** [[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: writeRegion|'''writeRegion''' - Write the alignments in the indexed BAM file that fall into the specified region and/or have the specified read name]] |
| + | ** [[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]] |
| + | |
| + | * Modify & write SAM/BAM Files |
| ** [[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: 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: 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: 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]]
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| * Informational Tools | | * Informational Tools |