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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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Fixing a bug when breaking up active regions where the resulting regions would overlap by one base. Adding quality score manipulation from the UG into the haplotype caller (qual capped by mapping quality, min qual threshold).
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2012-04-20 14:02:55 -04:00 |
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annotator
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PED support for Inbreeding Coefficient annotation
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2012-04-25 12:56:47 -04:00 |
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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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disabling all BQSR unit tests
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2012-04-30 14:39:55 -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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Exhaustive unit tests for Pool SNP genotype likelihoods:
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2012-04-30 14:29:46 -04:00 |
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indels
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Removing dependence on extended events from the RealignerTargetCreator. Did some minor refactoring while I was in there.
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2012-03-30 10:33:30 -04:00 |
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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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Added integration test for ValidationSiteSelector, correct MD5's
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2012-03-26 16:39:55 -04:00 |
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varianteval
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AC strat now checks if evals will be merged before throwing an error on multiple eval files.
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2012-04-19 16:08:55 -04:00 |
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variantrecalibration
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Removed experimental feature (aka hack) that was meant for 1000G consensus but remained in VQSR data manager - QD was being scaled by indel length. There's no evidence any more that QD is length-dependent, neither in CEU trio data nor in latest 1000G P2 calls
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2012-04-20 10:58:34 -04:00 |
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variantutils
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When running SelectVariants with the excludeNonVariants option, remove alleles from the ALT field that are no longer polymorphic.
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2012-04-20 14:30:04 -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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FlagStatIntegrationTest.java
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Adding integration test for Flag Stat
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2012-04-10 22:40:38 -04:00 |
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PileupWalkerIntegrationTest.java
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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.
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2012-04-02 14:27:36 -04:00 |
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PrintReadsIntegrationTest.java
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Bug fix for: https://getsatisfaction.com/gsa/topics/problem_with_indelrealigner_and_l_unmapped
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2012-04-27 09:58:38 -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 |
462450c3e3