amilev 0d94019bd6 Merge pull request #434 from broadinstitute/mc_dt_gccontent ... Add GC Content to DiagnoseTargets		2013-12-04 09:42:26 -08:00
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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	Bug fix for something Guillermo added to UG before he left to support calling indels from reduced reads.	2013-11-27 13:54:39 -05:00
haplotypecaller	Throw a GVCFIndexException when the user doesn't specify the optimal indexing strategy	2013-12-03 23:12:14 -05:00
indels	Bug fix for something Guillermo added to UG before he left to support calling indels from reduced reads.	2013-11-27 13:54:39 -05:00
phasing	Fixed bug in PhaseByTransmission where it was completely dropping multi-allelic records.	2013-08-21 15:46:57 -04:00
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	Various VQSR optimizations in both runtime and accuracy.	2013-11-29 13:04:46 -05:00
variantutils	Change the behavior of SelectVariants for PL/AD when it encounters a record that has lost one or more alternate alleles.	2013-12-03 09:23:03 -05:00