Eric Banks c7e08965d0 The QD normalization for indels was busted and is now fixed. ... It is true that indels of length > 1 have higher QUALS than those of length = 1. But for the HC those QUALS are not that much higher, and it doesn't continue scaling up as the indels get larger. So we no longer normalize by indel length (which massively over-penalizes larger events and effectively drops their QD to 0). For the UG the previous normalization also wasn't perfect. Now we divide the indel length by a factor of 3 to make sure that QD is consistent over the range of indel lengths. Integration tests change because QD is different for indels. Also, got permission from Valentin to archive a failing test that no longer applies. Thanks to Kurt on the GATK forum for pointing this all out.		2014-01-13 15:23:36 -05:00
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annotator	The QD normalization for indels was busted and is now fixed.	2014-01-13 15:23:36 -05:00
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	The QD normalization for indels was busted and is now fixed.	2014-01-13 15:23:36 -05:00
haplotypecaller	The QD normalization for indels was busted and is now fixed.	2014-01-13 15:23:36 -05:00
indels	Fixed edge condition in the realigner where a realigned read can sometimes get partially aligned off the end of the contig.	2014-01-08 00:37:28 -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