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== Getting Help ==
== Getting Help ==
If you have any questions please use the [http://groups.google.com/group/bamUtils bamUtil Google Group] to ask questions or recommend improvements to bamUtil.
If you have any questions please use the [https://github.com/statgen/bamUtil bamUtil GitHub page] to raise and issue.
See [[BamUtil: FAQ]] to see if your question has already been answered.
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.
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:
'''BamUtilLibStatGen.1.0.11 Release Notes'''
'''Version 1.0.14 - Released 7/8/2015'''
* Contains: [[LibStatGen Download#Official Releases|libStatGen version 1.0.11]] - see link for version updates
*[[LibStatGen Download#Official Releases|libStatGen version 1.0.14]]
* Contains: [[#Release of just BamUtil (does not include libStatGen)|bamUtil version 1.0.11]] - see link for version updates
*[[#Release of just BamUtil (does not include libStatGen)|bamUtil version 1.0.14]]
'''Older Releases'''
'''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
** Contains: [[#Release of just BamUtil (does not include libStatGen)|bamUtil 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
** Contains: [[LibStatGen Download#Official Releases|libStatGen version 1.0.11]] - see link for version updates
** Contains: [[#Release of just BamUtil (does not include libStatGen)|bamUtil version 1.0.11]] - see link for version updates
** Now properly supports 'B' & 'f' tags
** Cleanup - compile issues
*[[Media:BamUtilLibStatGen.1.0.10.tar.gz|BamUtilLibStatGen.1.0.10.tar.gz]] - Released 1/2/2014
*[[Media:BamUtilLibStatGen.1.0.10.tar.gz|BamUtilLibStatGen.1.0.10.tar.gz]] - Released 1/2/2014
** Contains: [[LibStatGen Download#Official Releases|libStatGen version 1.0.10]] - see link for version updates
** Contains: [[LibStatGen Download#Official Releases|libStatGen version 1.0.10]] - see link for version updates
To install an official release, unpack the downloaded file (tar xvf), cd into the bamUtil_x.x.x directory and type make all.
To install an official release, unpack the downloaded file (tar xvf), cd into the bamUtil_x.x.x directory and type make all.
* [[Media:BamUtil.1.0.11.tgz|BamUtil.1.0.11.tgz]] - Released 2/28/2014
'''BamUtil.1.0.14 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]]
** 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
** Update [[BamUtil: writeRegion|writeRegion]]
*** Add option to specify readnames to keep in a file
*** Fixed bug that if a read overlapped 2 BED positions, it was printed twice
** Update to [[BamUtil: bam2FastQ|bam2FastQ]]
*** Update to skip non-primary reads
** Update to [[BamUtil: polishBam|polishBam]]
*** Update to handle '\t' string inputs and to add CO option
*** Fix MD5sum calculation to convert fasta to uppercase prior to calculating
* [[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]]
** Update [[BamUtil: mergeBam|mergeBam]]
*** Add a regions option
** Update to [[BamUtil: squeeze|squeeze]], [[BamUtil: revert|revert]], [[BamUtil: diff|diff]]
*** Also accept ',' instead of just ';' as the delimiter in the input tags string.
* [[Media:BamUtil.1.0.11.tgz|BamUtil.1.0.11.tgz]] - Released 2/28/2014
* [[Media:BamUtil.1.0.11.tgz|BamUtil.1.0.11.tgz]] - Released 2/28/2014
** Requires, but does not include: [[LibStatGen Download#Official Releases|libStatGen version 1.0.11]]
** Requires, but does not include: [[LibStatGen Download#Official Releases|libStatGen version 1.0.11]]
*** Update compatibility with libStatGen due to 'B' & 'f' tag handling updates
*** Update compatibility with libStatGen due to 'B' & 'f' tag handling updates
** Add tests for 'B' & 'f' tags
** Add tests for 'B' & 'f' tags
* [[Media:BamUtil.1.0.10.tar.gz|BamUtil.1.0.10.tar.gz]] - Released 1/2/2014
* [[Media:BamUtil.1.0.10.tar.gz|BamUtil.1.0.10.tar.gz]] - Released 1/2/2014
**Initial release of just bamUtil. It started from the tool found in the deprecated StatGen repository.
**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]]
**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.]
= Programs =
= Programs =
