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| | The software reads the beginning of an input file to determine if it is SAM/BAM. To determine the format (SAM/BAM) of the output file, the software checks the output file's extension. If the extension is ".bam" it writes a BAM file, otherwise it writes a SAM file. | | The software reads the beginning of an input file to determine if it is SAM/BAM. To determine the format (SAM/BAM) of the output file, the software checks the output file's extension. If the extension is ".bam" it writes a BAM file, otherwise it writes a SAM file. |
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| − | The bam executable has the following functions.
| + | {{BamUtilPrograms}} |
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| − | * Rewrite SAM/BAM Files
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| − | ** [[BamUtil: convert|'''convert''' - Read a SAM/BAM file and write as a SAM/BAM file (optionally converts between '=' & bases in the sequence)]]
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| − | ** [[BamUtil: writeRegion|'''writeRegion''' - Write the alignments in the indexed BAM file that fall into the specified region and/or have the specified read name]]
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| − | ** [[BamUtil: splitChromosome|'''splitChromosome''' - Split BAM by Chromosome]]
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| − | ** [[BamUtil: splitBam|'''splitBam''' - Split SAM/BAM file by Read Group]]
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| − | ** [[BamUtil: findCigars|'''findCigars''' - Output just the reads that contain any of the specified CIGAR operations]]
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| − | * Modify & write SAM/BAM Files
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| − | ** [[BamUtil: clipOverlap|'''clipOverlap''' - Clip overlapping read pairs so they do not overlap]]
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| − | ** [[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]]
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| − | ** [[BamUtil: revert|'''revert''' - Revert SAM/BAM replacing the specified fields with their previous values (if known) and removes specified tags]]
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| − | ** [[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]]
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| − | ** [[BamUtil: trimBam|'''trimBam''' - Trim end of reads, changing read ends to ‘N’ & quality to ‘!’]]
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| − | **[[BamUtil: polishBam|'''polishBam''' – Add/Update header lines & add RG tag to each record]]
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| − | **[[BamUtil: rgMergeBam|'''rgMergeBam''' – Merge sorted BAM files adding Read Groups]]
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| − | **[[BamUtil: dedup|'''dedup''' – Mark or remove duplicates, can also perform recalibration]]
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| − | **[[BamUtil: recab|'''recab''' - Recalibrate base qualities]]
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| − | * Informational Tools
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| − | ** [[BamUtil: validate|'''validate''' - Read and Validate a SAM/BAM file]]
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| − | ** [[BamUtil: diff|'''diff''' - Print the diffs between 2 bams]]
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| − | ** [[BamUtil: stats|'''stats''' - Print some basic statistics on a SAM/BAM file]]
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| − | ** [[BamUtil: gapInfo|'''gapInfo''' - Print information on the gap between read pairs in a SAM/BAM file]]
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| − | * Print Information in Readable Form:
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| − | ** [[BamUtil: dumpHeader|'''dumpHeader''' - Print SAM/BAM header]]
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| − | ** [[BamUtil: dumpRefInfo|'''dumpRefInfo''' - Print SAM/BAM Reference Information]]
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| − | ** [[BamUtil: dumpIndex|'''dumpIndex''' - Dump a BAM index file into an easy to read text version]]
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| − | ** [[BamUtil: readReference|'''readReference''' - Print the reference string for the specified region]]
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| − | *Additional Tools
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| − | ** [[BamUtil: bam2FastQ|'''bam2FastQ''' - Convert the specified BAM file to fastQs]]
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| − | * Dummy/Example Tools:
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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]]
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| − | This executable is built using [[C++ Library: libStatGen]].
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| − | Just running ./bam will print the Usage information for the bam executable.
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