..
CNV
Updating md5 because the file changed
2011-09-23 07:33:20 -04:00
activeregionqc
There are now three triggering options in the HaplotypeCaller. The default (mismatches, insertions, deletions, high quality soft clips), an external alleles file (from the UG for example), or extended triggers which include low quality soft clips, bad mates and unmapped mates. Added better algorithm for band pass filtering an ActivityProfile and breaking them apart when they get too big. Greatly increased the specificity of the caller by battening down the hatches on things like base quality and mapping quality thresholds for both the assembler and the likelihood function.
2012-04-10 14:48:23 -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
Improved BQSR plotting and some new parameters
2012-04-19 09:31:41 -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
Khalid pressured me into adding an integration test that makes sure we don't fail on reads with adjacent I and D events.
2012-04-17 21:21:29 -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
Update VE IT to reflect new fields and bugfixes
2012-04-13 17:00:37 -04:00
variantrecalibration
Final tweaks. Added an integration test to cover the case of SNPs and indels that start at the same position.
2012-04-17 23:54:10 -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
FlagStatIntegrationTest.java
Adding integration test for Flag Stat
2012-04-10 22:40:38 -04:00
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
Reorganized the codebase beneath top-level public and private directories,
2011-06-28 06:55:19 -04:00
PrintReadsUnitTest.java
Better location for the downsampling of reads in PrintReads
2012-01-14 14:06:09 -05:00
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