Mark DePristo b7d1096ced Added onlyEmitSamples argument to UnifiedGenotyper ... -- When provided, this argument causes us to only emit the selected samples into the VCF. No INFO field annotations (AC for example) or other features are modified. It's current primary use is for efficiently evaluating joint calling. -- Add integration test for onlyEmitSamples		2013-08-09 11:00:15 -04:00
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annotator	moved SnpEffUtilUnitTest to public tree	2013-07-30 17:51:40 -04:00
beagle	Simpler FILTER and info field encoding for BeagleOutputToVCF	2013-06-14 15:56:13 -04:00
bqsr	Removed plots generation from the BaseRecalibration software	2013-06-19 14:47:56 -04:00
compression/reducereads	Two reduce reads updates/fixes:	2013-08-01 14:34:59 -04:00
diagnostics	Update MD5s and the Diagnose Target scala script	2013-05-13 12:06:17 -04:00
diffengine	Fixed issues raised by Appistry QA (mostly small fixes, corrections & clarifications to GATKDocs)	2013-03-12 10:57:14 -04:00
fasta	Updated all JAVA file licenses accordingly	2013-01-10 17:06:41 -05:00
filters	Don't allow users to specify keys and IDs that contain angle brackets or equals signs (not allowed in VCF spec).	2013-04-05 00:52:32 -04:00
genotyper	Added onlyEmitSamples argument to UnifiedGenotyper	2013-08-09 11:00:15 -04:00
haplotypecaller	Bugfix for ReferenceConfidenceModel	2013-08-06 16:00:32 -04:00
indels	Another fix for the Indel Realigner that arises because of secondary alignments.	2013-06-21 16:59:22 -04:00
phasing	Updated all JAVA file licenses accordingly	2013-01-10 17:06:41 -05:00
validation	MathUtils.randomSubset() now uses Collections.shuffle() (indirectly, through the other methods	2013-03-29 14:52:10 -04:00
varianteval	Move some VCF/VariantContext methods back to the GATK based on feedback	2013-01-29 16:56:55 -05:00
variantrecalibration	Separate num Gaussians for + and - GMM in VQSR	2013-08-07 07:36:50 -04:00
variantutils	CombineVariants no longer adds PASS to unfiltered records	2013-05-20 16:53:51 -04:00