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BamUtil

129 bytes added, 10:39, 6 March 2012
Programs
* 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: writeRegion|'''writeRegion''' - Write the alignments in the indexed BAM file that fall into the specified region and/or have the specified read name]]
** [[BamUtil: splitChromosome|'''splitChromosome''' - Split BAM by Chromosome]]
** [[BamUtil: writeRegionsplitBam|'''writeRegionsplitBam''' - Write the alignments in the indexed Split SAM/BAM file that fall into the specified region and/or have the specified read nameby Read Group]]
** [[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]]
** [[BamUtil: splitBam|'''splitBam''' - Split SAM/BAM file by Read Group]]
* Modify & write SAM/BAM Files
** [[BamUtil: clipOverlap|'''clipOverlap''' - Clip overlapping read pairs so they do not overlap]]
** [[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''' - Reduce file 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]]
* Informational Tools
** [[BamUtil: diff|'''diff''' - Print the diffs between 2 bams]]
** [[BamUtil: stats|'''stats''' - Print some basic statistics on a SAM/BAM file]]
** [[BamUtil: gapInfo|'''gapInfo''' - Print information on the gap between read pairs in a SAM/BAM file]]
* Print Information in Readable Form:
** [[BamUtil: readReference|'''readReference''' - Print the reference string for the specified region]]
* 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]]
This executable is built using [[C++ Library: libStatGen]].
Just running ./bam will print the Usage information for the bam executable.

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