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CNV
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Updating md5 because the file changed
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2011-09-23 07:33:20 -04:00 |
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activeregionqc
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CountReadsInActiveRegions now emits a detailed GATK report
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2012-03-14 17:26:37 -04:00 |
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annotator
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Updating integration tests now that standard annotations support multiple alleles
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2012-02-27 11:32:26 -05:00 |
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beagle
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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=./. .)
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2012-01-23 08:25:34 -05:00 |
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bqsr
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Updated read group covariate to use sample.lane instead of the id
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2012-03-23 15:24:07 -04:00 |
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coverage
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DoC now properly handles reference N bases + misc. additional cleanups
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2012-02-25 11:32:50 -05:00 |
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diagnostics
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GATKReport v1.0
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2012-03-12 23:09:19 -04:00 |
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diffengine
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Fixing MD5's (new GATKReport header was missing from old md5's)
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2012-03-19 15:28:45 -04:00 |
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fasta
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Removing the legacy -L "interval1;interval2" syntax
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2011-11-21 13:18:53 -05:00 |
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filters
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Again, fixing the add call when we really mean replace
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2011-11-21 19:15:56 -05:00 |
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genotyper
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Resolving conflicts
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2012-03-16 14:36:07 -04:00 |
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indels
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Rename *PerformanceTest test classes to *LargeScaleTest
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2011-12-22 10:38:49 -05:00 |
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phasing
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Added respectPhaseInInput flag to RBP and integration tests
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2012-03-22 17:40:21 -04:00 |
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qc
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First version of VariantContextBuilder
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2011-11-18 11:06:15 -05:00 |
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recalibration
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Patching special case in the adaptor clipping
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2012-01-11 17:47:44 -05:00 |
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validation
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Removing all instances of -BTI (in tests and in GATKdocs) and replacing them with the appropriate alternative.
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2011-10-27 23:55:11 -04:00 |
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varianteval
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Unified, standard IndelSummary metrics for VariantEval
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2012-03-22 21:24:37 -04:00 |
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variantrecalibration
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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.
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2011-09-12 12:17:43 -04:00 |
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variantutils
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Merged bug fix from Stable into Unstable
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2012-03-21 12:44:43 -04:00 |
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BAQIntegrationTest.java
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merge master
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2011-10-25 16:08:39 -04:00 |
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ClipReadsWalkersIntegrationTest.java
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Updating MD5s for updated BAM with read groups
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2011-10-06 12:15:48 -07:00 |
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PileupWalkerIntegrationTest.java
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Updated integration tests for the new adaptor clipping fix.
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2011-12-30 18:47:14 -05:00 |
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PrintReadsIntegrationTest.java
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Reorganized the codebase beneath top-level public and private directories,
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2011-06-28 06:55:19 -04:00 |
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PrintReadsUnitTest.java
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Better location for the downsampling of reads in PrintReads
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2012-01-14 14:06:09 -05:00 |
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