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BamUtil

210 bytes added, 14:58, 2 September 2011
Reorganize the tools
The bam executable has the following functions.
  * [[BamUtil: validate|validate|validate - Read and Validate a Rewrite SAM/BAM file]]Files** [[BamUtil: convert|convert - Read a SAM/BAM file and write as a SAM/BAM file (optionally converts between '=' & bases in the sequence)]]* [[BamUtil: dumpHeader|dumpHeader - Print SAM/BAM header]]* [[BamUtil: splitChromosome|splitChromosome - Split BAM by Chromosome]]** [[BamUtil: writeRegion|writeRegion - Write the alignments in the indexed BAM file that fall into the specified regionand/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: dumpRefInforevert|dumpRefInfo revert - Print Revert SAM/BAM Reference Informationreplacing the specified fields with their previous values (if known) and removes specified tags]]** [[BamUtil: dumpIndexsqueeze|dumpIndex squeeze - Dump reduces files size by dropping OQ fields, duplicates, specified tags, using '=' when a BAM index file into an easy to read text versionbase 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: filtervalidate|validate|filter validate - Filter reads by clipping ends with too high of Read and Validate a mismatch percentage and by marking reads unmapped if the quality of mismatches is too highSAM/BAM file]]** [[BamUtil: readReferencediff|readReference diff - Print the reference string for the specified regiondiffs between 2 bams]]** [[BamUtil: diffstats|diff stats - Print the diffs between 2 bams]] * Print Information in Readable Form:** [[BamUtil: statsdumpHeader|stats dumpHeader - Print the diffs between 2 bamsSAM/BAM header]]** [[BamUtil: revertdumpRefInfo|revert dumpRefInfo - Revert Print SAM/BAM replacing the specified fields with their previous values (if known).Reference Information]]** [[BamUtil: squeezedumpIndex|squeeze dumpIndex - reduces files size by dropping OQ fields, duplicates, specified tags, using '=' when Dump a base matches the reference, binning quality scores.BAM index file into an easy to read text version]]** [[BamUtil: findCigarsreadReference|findCigars readReference - Output just Print the reads that contain any of reference string for the specified CIGAR operations.region]] 
This executable is built using [[C++ Library: libStatGen]].
Just running ./bam will print the Usage information for the bam executable.

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