Line 10: |
Line 10: |
| == 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. |
− | | |
− | Alternatively, you can e-mail me, Mary Kate Wing, at mktrost@umich.edu.
| |
| | | |
| See [[BamUtil: FAQ]] to see if your question has already been answered. | | See [[BamUtil: FAQ]] to see if your question has already been answered. |
Line 29: |
Line 27: |
| 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: |
| | | |
− | [[Media:BamUtilLibStatGen.1.0.13.tgz|BamUtilLibStatGen.1.0.13.tgz]] - Released 2/20/2015
| |
| | | |
− | '''BamUtilLibStatGen.1.0.13 Release Notes''' | + | '''Version 1.0.14 - Released 7/8/2015''' |
− | * Contains: [[LibStatGen Download#Official Releases|libStatGen version 1.0.13]] - 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 1.0.13]] - 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 | | * [[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: [[LibStatGen Download#Official Releases|libStatGen version 1.0.12]] - see link for version updates |
Line 43: |
Line 46: |
| ** Adds regions to [[BamUtil: mergeBam|mergeBam]] | | ** Adds regions to [[BamUtil: mergeBam|mergeBam]] |
| ** Accept ',' delimiters for the tags string input in [[BamUtil: squeeze|squeeze]], [[BamUtil: revert|revert]], & [[BamUtil: diff|diff]] | | ** 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 | | *[[Media:BamUtilLibStatGen.1.0.11.tar.gz|BamUtilLibStatGen.1.0.11.tar.gz]] - Released 2/28/2014 |
Line 251: |
Line 253: |
| **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 = |