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2,951 bytes removed, 14:23, 3 January 2014
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 bam executable has the following functions.  * 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: splitBam|'''splitBam''' - Split SAM/BAM file by Read Group]]** [[BamUtil: findCigars|'''findCigars''' - Output just the reads that contain any of the specified CIGAR operations]] * 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: trimBam|'''trimBam''' - Trim end of reads, changing read ends to ‘N’ & quality to ‘!’]]**[[BamUtil: polishBam|'''polishBam''' – Add/Update header lines & add RG tag to each record]]**[[BamUtil: rgMergeBam|'''rgMergeBam''' – Merge sorted BAM files adding Read Groups]]**[[BamUtil: dedup|'''dedup''' – Mark or remove duplicates, can also perform recalibration]]**[[BamUtil: recab|'''recab''' - Recalibrate base qualities]] * Informational Tools** [[BamUtil: validate|'''validate''' - Read and Validate a SAM/BAM file]]** [[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: 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]] *Additional Tools** [[BamUtil: bam2FastQ|'''bam2FastQ''' - Convert the specified BAM file to fastQs]] * 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.{{BamUtilPrograms}}

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