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| == Getting Help == | | == Getting Help == |
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− | 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. |
− | | |
− | Alternatively, you can e-mail me, Mary Kate Wing, at mktrost@umich.edu.
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| + | See [[BamUtil: FAQ]] to see if your question has already been answered. |
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| == Where to Find It == | | == Where to Find It == |
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| 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. |
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| + | For version 1.0.14 and later, please download libStatGen and bamUtil separately: |
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− | [[Media:BamUtilLibStatGen.1.0.11.tar.gz|BamUtilLibStatGen.1.0.11.tar.gz]] - Released 2/28/2014
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− | '''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]] |
− | * Now properly supports 'B' & 'f' tags
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− | * Cleanup - compile issues
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| '''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 |
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| 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. |
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− | * [[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. |
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− | '''BamUtil.1.0.11 Release Notes'''
| |
| * [[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]] |
| + | *** Adds support for 'B' & 'f' tags that did not work properly before. |
| ** Update [[BamUtil: splitBam|splitBam]] & [[BamUtil: polishBam|polishBam]] | | ** Update [[BamUtil: splitBam|splitBam]] & [[BamUtil: polishBam|polishBam]] |
| *** Update to work properly if log & output file are not specified (no longer creates '.log') | | *** Update to work properly if log & output file are not specified (no longer creates '.log') |
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| *** 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 |
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− | '''Older Releases'''
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| * [[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 |
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| **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]] |
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| + | == 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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| = Programs = | | = Programs = |