| .. |
|
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
|
fixed estimated Q reported calculation in the gatherer
|
2012-03-29 12:28:43 -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
|
UG integration tests updated. A handful of sites are lost because there are only 5 indels and one starts at the beginning of the read so it no longer passes our min threshold (now consistent with GGA), but mostly the depth changes ever so slightly once in a while between extended and normal pileups (I think the normal pileups are correct). I have looked thoroughly in IGV at ALL differences and am happy with the new results. As an aside, the AD is now calculated more accurately for indels.
|
2012-03-30 01:35:49 -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
|
Final commits to VariantEval
|
2012-03-30 20:11:06 -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
|
Updated integration tests for the new adaptor clipping fix.
|
2011-12-30 18:47:14 -05:00 |
|
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 |
4f73ea902f