3,045
edits
Changes
From Genome Analysis Wiki
Jump to navigationJump to search→Release of just BamUtil (does not include libStatGen)
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.
'''BamUtil.1.0.13 Release Notes'''
'''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
* BamUtil Version 1.0.13 - Released 2/20/2015
** https://github.com/statgen/bamUtil/archive/v1.0.13.tar.gz
** 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]]
** Requires, but does not include: [[LibStatGen Download#Official Releases|libStatGen version 1.0.13]]
** Makefule Updates
** Makefile Updates
*** Improve logic to determine actual path for the library
*** Improve logic to determine actual path for the library
*** Update to append to USER_COMPILE_VARS even if specified on the command line
*** 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
*** 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
* [[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]]
** Requires, but does not include: [[LibStatGen Download#Official Releases|libStatGen version 1.0.12]]
