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BamUtil

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== Getting Help ==
If you have any questions please use the [httphttps://groups.googlegithub.com/groupstatgen/bamUtils bamUtil Google GroupbamUtil GitHub page] to ask questions or recommend improvements to bamUtil. Alternatively, you can e-mail me, Mary Kate Wing, at mktrost@umich.eduraise and issue.
See [[BamUtil: FAQ]] to see if your question has already been answered.
To install an official release, unpack the downloaded file (tar xvf), cd into the bamUtil_x.x.x directory and type make all.
For version 1.0.14 and later, please download libStatGen and bamUtil separately:
[[Media:BamUtilLibStatGen.1.0.13.tar.gz|BamUtilLibStatGen.1.0.13.tgz‎]] - Released 2/20/2015
'''BamUtilLibStatGen.Version 1.0.13 Release Notes14 - Released 7/8/2015'''* Contains: [[LibStatGen Download#Official Releases|libStatGen version 1.0.1314]] - see link for version updates* Contains: [[#Release of just BamUtil (does not include libStatGen)|bamUtil version 1.0.1314]] - see link for version updates
'''Older Releases'''
* [[Media:BamUtilLibStatGen.1.0.13.tgz|BamUtilLibStatGen.1.0.13.tgz‎]] - Released 2/20/2015
** Contains: [[LibStatGen Download#Official Releases|libStatGen version 1.0.13]] - see link for version updates
** Contains: [[#Release of just BamUtil (does not include libStatGen)|bamUtil version 1.0.13]] - see link for version updates
 
 
* [[Media:BamUtilLibStatGen.1.0.12.tar.gz|BamUtilLibStatGen.1.0.12.tgz‎]] - Released 5/14/2014
** Contains: [[LibStatGen Download#Official Releases|libStatGen version 1.0.12]] - see link for version updates
** Adds regions to [[BamUtil: mergeBam|mergeBam]]
** Accept ',' delimiters for the tags string input in [[BamUtil: squeeze|squeeze]], [[BamUtil: revert|revert]], & [[BamUtil: diff|diff]]
 
*[[Media:BamUtilLibStatGen.1.0.11.tar.gz|BamUtilLibStatGen.1.0.11.tar.gz‎]] - Released 2/28/2014
To install an official release, unpack the downloaded file (tar xvf), cd into the bamUtil_x.x.x directory and type make all.
'''BamUtil.1.0.13 14 Release Notes'''* BamUtil Version 1.0.14 - Released 7/8/2015** https://github.com/statgen/bamUtil/archive/v1.0.14.tar.gz** Requires, but does not include: [[LibStatGen Download#Official Releases|libStatGen version 1.0.14]]** Update [[BamUtil: trimBam|trimBam]]*** Add option to soft clip (-c) instead of trimming** Update [[BamUtil: clipOverlap|clipOverlap]]*** Add option to mark reads as unmapped if they are entirely clipped** Update to [[BamUtil: bam2FastQ|bam2FastQ]]*** Add option to gzip the output files*** Add option to split Read Groups into separate fastq files*** Add option to get the quality from a tag** Update [[BamUtil: recab|recab]]*** Update to ignore ref 'N' when building the recalibration table*** Add ability to bin** Add Dedup_LowMem tool '''Older Releases'''
* BamUtil Version 1.0.13 - Released 2/20/2015
** https://github.com/statgen/bamUtil/archive/v1.0.13.tar.gz
** Requires, but does not include: [[LibStatGen Download#Official Releases|libStatGen version 1.0.13]]
** Makefule Makefile Updates
*** Improve logic to determine actual path for the library
*** Update to append to USER_COMPILE_VARS even if specified on the command line
*** Fix MD5sum calculation to convert fasta to uppercase prior to calculating
'''Older Releases'''
* [[Media:BamUtil.1.0.12.tgz|BamUtil.1.0.12.tgz‎]] - Released 5/14/2014
** Requires, but does not include: [[LibStatGen Download#Official Releases|libStatGen version 1.0.12]]
**Initial release of just bamUtil. It started from the tool found in the deprecated StatGen repository.
**Contains: [[BamUtil: validate|validate]], [[BamUtil: convert|convert]], [[BamUtil: dumpHeader|dumpHeader]], [[BamUtil: splitChromosome|splitChromosome]], [[BamUtil: writeRegion|writeRegion]], [[BamUtil: dumpRefInfo|dumpRefInfo]], [[BamUtil: dumpIndex|dumpIndex]], [[BamUtil: readIndexedBam|readIndexedBam]], [[BamUtil: filter|filter]], [[BamUtil: readReference|readReference]], [[BamUtil: revert|revert]], [[BamUtil: diff|diff]], [[BamUtil: squeeze|squeeze]], [[BamUtil: findCigars|findCigars]], [[BamUtil: stats|stats]]
 
== Citation ==
If you use BamUtil, please cite our publication on GotCloud which includes BamUtil:
[http://genome.cshlp.org/content/early/2015/04/14/gr.176552.114.abstract Jun, Goo, et al. "An efficient and scalable analysis framework for variant extraction and refinement from population scale DNA sequence data." Genome research (2015): gr-176552.]
 
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