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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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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 |
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