Ryan Poplin 856c1f87c1 Allow for additional input data to be used in the VQSR for clustering but don't carry it forward into the output VCF file. ... -- New -a argument in the VQSR for specifying additional data to be used in the clustering -- New NA12878KB walker which creates ROC curves by partitioning the data along VQSLOD and calculating how many KB TP/FP's are called.		2014-01-02 14:46:04 -05:00
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annotator	Improvements to the reference model pipeline.	2013-11-01 17:58:25 -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	Bug fix for RR: stop (incorrectly) pulling the MQ out of the SAMRecord as a byte instead of an int.	2013-11-27 18:55:03 -05:00
diagnostics	Add GC Content to DiagnoseTargets	2013-12-03 23:04:40 -05:00
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	Fixed up edge condition for clipping long reads in the HMM.	2014-01-01 19:05:09 -05:00
haplotypecaller	Fixed issue > 0 log likelihoods using GraphBased likelihood engine reported by Mauricio	2013-12-13 11:19:57 -05:00
indels	Fixed up edge condition for clipping long reads in the HMM.	2014-01-01 19:05:09 -05:00
phasing	Fixed bug in PhaseByTransmission where it was completely dropping multi-allelic records.	2013-08-21 15:46:57 -04:00
rnaseq	Write a new tool for spliting reads that have N cigar string.	2014-01-01 22:21:36 -05:00
validation	MathUtils.randomSubset() now uses Collections.shuffle() (indirectly, through the other methods	2013-03-29 14:52:10 -04:00
varianteval	adding a check for the UNAVAILABLE case of GenotypeType in CountVariants	2013-08-29 17:27:00 -04:00
variantrecalibration	Allow for additional input data to be used in the VQSR for clustering but don't carry it forward into the output VCF file.	2014-01-02 14:46:04 -05:00
variantutils	Created a new walker to do the full combination of N gVCFs from the HC single-sample ref calc pipeline.	2013-12-31 12:07:56 -05:00