Eric Banks 10e74a71eb We now allow arbitrary annotations other than dbSNP (e.g. HM3) to come out of the Unified Genotyper. This was already set up in the Variant Annotator Engine and was just a matter of hooking UG up to it. Added integration test to ensure correct behavior.		2012-04-10 12:30:35 -04:00
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CNV	Updating md5 because the file changed	2011-09-23 07:33:20 -04:00
activeregionqc	CountReadsInActiveRegions now emits a detailed GATK report	2012-03-14 17:26:37 -04:00
annotator	Updating integration tests now that standard annotations support multiple alleles	2012-02-27 11:32:26 -05:00
beagle	Minor tweaks to T2D-related qscripts. Replacing old md5s from the BeagleIntegrationTest. All differences boiled down either to the accounting of genotypes changed (./. --> 0/0 is no longer a "changed" genotype, and original genotypes that were ./. are represented as OG=. rather than OG=./. .)	2012-01-23 08:25:34 -05:00
bqsr	BQSR bug triage	2012-04-05 09:32:18 -04:00
coverage	DoC now properly handles reference N bases + misc. additional cleanups	2012-02-25 11:32:50 -05:00
diagnostics	GATKReport v1.0	2012-03-12 23:09:19 -04:00
diffengine	Fixing MD5's (new GATKReport header was missing from old md5's)	2012-03-19 15:28:45 -04:00
fasta	Removing the legacy -L "interval1;interval2" syntax	2011-11-21 13:18:53 -05:00
filters	Again, fixing the add call when we really mean replace	2011-11-21 19:15:56 -05:00
genotyper	We now allow arbitrary annotations other than dbSNP (e.g. HM3) to come out of the Unified Genotyper. This was already set up in the Variant Annotator Engine and was just a matter of hooking UG up to it. Added integration test to ensure correct behavior.	2012-04-10 12:30:35 -04:00
indels	Removing dependence on extended events from the RealignerTargetCreator. Did some minor refactoring while I was in there.	2012-03-30 10:33:30 -04:00
phasing	Added respectPhaseInInput flag to RBP and integration tests	2012-03-22 17:40:21 -04:00
qc	First version of VariantContextBuilder	2011-11-18 11:06:15 -05:00
recalibration	Patching special case in the adaptor clipping	2012-01-11 17:47:44 -05:00
validation	Added integration test for ValidationSiteSelector, correct MD5's	2012-03-26 16:39:55 -04:00
varianteval	Improvements to indel analysis capabilities of VariantEval	2012-04-06 16:07:46 -04:00
variantrecalibration	Changing the VQSR command line syntax back to the parsed tags approach. This cleans up the code and makes sure we won't be parsing the same rod file multiple times. I've tried to update the appropriate qscripts.	2011-09-12 12:17:43 -04:00
variantutils	Final update for VE. VCFStreaming wasn't yet updated	2012-03-30 21:52:01 -04:00
BAQIntegrationTest.java	merge master	2011-10-25 16:08:39 -04:00
ClipReadsWalkersIntegrationTest.java	Updating MD5s for updated BAM with read groups	2011-10-06 12:15:48 -07:00
PileupWalkerIntegrationTest.java	Had some free time, so I unplugged extended events from the walkers. Now they exist only in LocusIteratorByState, but ReadProperties.generateExtendedEvents() always returns false so that block is never actually executed anymore. I don't want to touch LIBS because I think David is in there right now.	2012-04-02 14:27:36 -04:00
PrintReadsIntegrationTest.java	…
PrintReadsUnitTest.java	Better location for the downsampling of reads in PrintReads	2012-01-14 14:06:09 -05:00