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For information on installing the releases, see: [[GotCloud#Install_GotCloud_Software|Install GotCloud Software]]
For information on installing the releases, see: [[GotCloud#Install_GotCloud_Software|Install GotCloud Software]]
For information on issues/resolutions for specific versions, see: [[GotCloud:_FAQs#Version_Problems|FAQ: Version Problems]]
For information on issues/resolutions for specific versions, see: [[GotCloud:_FAQs#Version_Problems|FAQ: Version Problems]]
== Version 1.12 (Full Release on 1/17/2014) ==
''' General '''
* GotCloud now works when installed in a bin/ directory.
* Add tabix source and build & bgzip build
* Add some Copyright information
* Fix printing of a failed run's return code
* Upgrade to latest [[LibStatGen_Download#Official Releases|libStatGen]] & [[BamUtil#Release_of_just_BamUtil_.28does_not_include_libStatGen.29|bamUtil]]
** Slightly newer than 1.0.10 for both - versions on 1/17/2014.
** dedup & recab now ignore Secondary reads
** mergeBam ignores PI header field when merging
** Add PhoneHome - gotCloud applies a PhoneHome thinning (BAMUTIL_THINNING) defaulted to 10 (10% of the time bamUtil does PhoneHome)
* Upgrade QPLOT to ignore secondary reads
* samtools
** Update samtools index to return an error code if it fails to build the index
'''Aligner'''
* Updgrade BWA
** BWA_MEM is now an option
* Write timestamps to Makefile log as steps start & complete
* Remove tmp files as gotCloud goes, rather than at the end.
* Deprecate RUN_QPLOT & RUN_VERIFY_BAM_ID
** Now the steps to run are specified in configuration.
* Mosaik
** Upgrade to version from Oct 29, 2013
** Add premo for pre-Mosaik processing
'''Variant Calling'''
* Update to properly handle empty VCFs
* Run make with -k option to run as much as possible after a failure.
* Update to allow steps to be dependent on BAMs (BAM_DEPEND) so they will rerun if a BAM has a newer timestamp.
* Input Validation
** Check that BAMs exist & are not empty prior to running steps that require BAMs.
** Check that filters min/maxDP are numbers, not fractions.
* GlfMultiples
** update to use DP instead of GD and fix PL description in format field header
** add region option
* samtools-hybrid
** fail on missing BGZF EOF indicator
'''Genotype Refinement'''
* Add a default number of states to Thunder
== Version 1.11 (Full Release on 9/6/2013) ==
== Version 1.11 (Full Release on 9/6/2013) ==
