kshakir 307c8ca027 Created a new playground script for cleaning bams in Firehose. ... Some refactoring of Queue extensions for reusability in scripts. Putting the extensions into the Queue.jar after building them. More updates to GATK walker arguments specifying @Input and @Output for Queue. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4032 348d0f76-0448-11de-a6fe-93d51630548a		2010-08-13 23:52:24 +00:00
..
Aligner.xml	Cleanup and formatting overhaul.	2010-01-21 19:22:56 +00:00
AnalyzeConcordance.xml	Added a playground concordance analyzer for summarizing VariantEval across a group.	2010-02-22 20:28:52 +00:00
AnalyzeCovariates.xml	A few more bug fixes based on extended testing. Sorry, Eric.	2010-01-21 22:12:16 +00:00
CreatePackager.xsl	Tweak the layout of the resulting .tar.bz2 a bit.	2010-01-27 22:07:37 +00:00
FindContaminatingReadGroups.xml	Cleanup and formatting overhaul.	2010-01-21 19:22:56 +00:00
GATK-Picard.xml	A few more bug fixes based on extended testing. Sorry, Eric.	2010-01-21 22:12:16 +00:00
GATKResources.xml	Updated resources package descriptor with dbsnp 129 for b37.	2010-08-03 02:42:48 +00:00
GenomeAnalysisTK.xml	It's probably a good idea to look carefully at what you've done before actually committing	2010-07-23 17:06:54 +00:00
IndelGenotyper.xml	Bringing IndelGenotyper back to life	2010-02-03 20:12:49 +00:00
LocalRealignmentAroundIndels.xml	Since IntervalCleaner is gone for good, it is sensible to update the package to refer to the new IndelRealigner instead	2010-02-24 16:42:56 +00:00
PicardPrivate.xml	Update to the latest rev of the picard sharding patch. Includes updates reflecting	2010-06-06 20:33:21 +00:00
QualityScoresRecalibration.xml	A few more bug fixes based on extended testing. Sorry, Eric.	2010-01-21 22:12:16 +00:00
Queue.xml	Created a new playground script for cleaning bams in Firehose.	2010-08-13 23:52:24 +00:00
UnifiedGenotyper.xml	Cleanup and formatting overhaul.	2010-01-21 19:22:56 +00:00
VariantAnnotator.xml	Adding HaplotypeScore to the VariantAnnotator package (so it can be used with Firehose)	2010-04-14 18:37:21 +00:00
VariantEval.xml	Add CountFunctionalVariants to local release (for firehose)	2010-07-17 01:36:16 +00:00
VariantFiltration.xml	Temporary solution: add the commons logging implementation to the VariantFiltration package. Downstream solution is described in GSA-262.	2010-01-23 01:46:18 +00:00
VariantRecalibration.xml	VariantOptimizer package is moved to core, renamed as VariantRecalibration, and added to the binary release package. VariantOptimizer walker is renamed to GenerateVariantClustersWalker and ApplyVariantClustersWalker renamed to VariantRecalibrator. Integration tests added, performance tests still to be done.	2010-05-28 18:20:18 +00:00