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broadinstitute
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gatk-protected
Obsolete/Legacy GATK repository -- go to https://github.com/broadinstitute/gatk instead
BSD 3-Clause "New" or "Revised" License
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TargetCoverageSexGenotyper and PAR regions
#1085
mbabadi
closed
7 years ago
1
adding argument --onlyOutputCallsStartingInIntervals to GenotypeGVCFs
#1084
lbergelson
closed
7 years ago
0
Mutect2: only output calls that *start* in the current shard
#1083
droazen
closed
7 years ago
1
CNV ConvertBedToTargetFile: tag doc, give example command and pad intro
#1082
sooheelee
closed
7 years ago
2
duplicate haplotype caller start position bug fix in mutect
#1081
lbergelson
closed
7 years ago
0
CNV ConvertACNVResults: tag doc, give example command, question summary
#1080
sooheelee
closed
7 years ago
6
CNV AnnotateTargets: Shl doc annotate targets
#1079
sooheelee
closed
7 years ago
1
CNV CallSegments: tag doc and give example command
#1078
sooheelee
closed
7 years ago
1
CNV PlotSegmentedCopyRatio: tag doc, add example command, clarify -SD parameter
#1077
sooheelee
closed
7 years ago
8
Added germline CNV WDL workflows
#1076
asmirnov239
opened
7 years ago
6
CNV PerformSegmentation: tag doc, note R requirement and give example commands
#1075
sooheelee
closed
7 years ago
3
CNV NormalizeSomaticReadCounts: tag doc and provide example command
#1074
sooheelee
closed
7 years ago
8
CNV CreatePanelOfNormals: tag doc, add example command
#1073
sooheelee
closed
7 years ago
3
CNV CombineReadCounts: tag doc
#1072
sooheelee
closed
7 years ago
1
Instrumentation and ICG function evaluation counts in gCNV
#1071
mbabadi
closed
7 years ago
1
Clean up and update CNV methods documentation
#1070
mbabadi
closed
7 years ago
1
Tumor-in-normal and PoN creation from mixed-N/T cohorts
#1069
mbabadi
closed
7 years ago
1
CNV SparkGenomeReadCounts tag doc; example WGS command
#1068
sooheelee
closed
7 years ago
9
CNV CalculateTargetCoverage: tag doc; example WES command; change defaults
#1067
sooheelee
closed
7 years ago
14
Migrate to Nd4j BLAS
#1066
mbabadi
closed
7 years ago
1
Write integration test for GermlineCNVCaller for single sample calling
#1065
asmirnov239
closed
7 years ago
6
Limit the number of copy number states and designate a special state to capture all higher copy number states
#1064
mbabadi
closed
7 years ago
1
Replace or remove Nd4jUtils.getNDArrayByIndices() method
#1063
asmirnov239
closed
7 years ago
1
More flexible integer copy number transition priors in gCNV
#1062
mbabadi
closed
7 years ago
1
Evaluate the necessity for external GC correction vs. depending on the coverage model for ab initio discovery of GC bias
#1061
mbabadi
closed
7 years ago
1
Eliminated other erroneous ploidy errors.
#1060
LeeTL1220
closed
7 years ago
0
Use Nd4j workspaces for better memory management
#1059
mbabadi
closed
7 years ago
1
gCNV default parameters
#1058
mbabadi
closed
7 years ago
1
gCNV genotyping tool
#1057
mbabadi
closed
7 years ago
1
Viterbi vs. local posteriors
#1056
mbabadi
closed
7 years ago
1
ReadCountCollection pre-processing filters
#1055
mbabadi
closed
7 years ago
1
Add warning message to add allele specific annotation group
#1054
ronlevine
closed
7 years ago
4
Docker image to use openjdk8
#1053
LeeTL1220
closed
7 years ago
1
Update to 4.alpha.2-272-gf4d928f-20170517.201327-1
#1052
lbergelson
closed
7 years ago
2
Go through M2 isActive results in IGV
#1051
davidbenjamin
closed
7 years ago
1
Fix JointAFCRSegmenterUnitTest.
#1050
samuelklee
closed
7 years ago
1
CNV AllelicCNV: Shl doc alleliccnv
#1049
sooheelee
closed
7 years ago
11
Doc generation fails on tools that use classes in cachemanager package
#1048
sooheelee
closed
7 years ago
6
updating gatk to 4.alpha.2-271-gb05aee6-20170517.012235-1
#1047
lbergelson
closed
7 years ago
2
Fixing issue in OB filter that caused crash when erroneously detectin…
#1046
LeeTL1220
closed
7 years ago
1
Applying GATK to microbiome data
#1045
sooheelee
closed
7 years ago
6
FilterByOrientationBias will fail when it (erroneously) determines that it is running on a non-diploid organism.
#1044
LeeTL1220
closed
7 years ago
3
M2 WDL does not fail if a single command line fails in the Filter task
#1043
LeeTL1220
closed
7 years ago
0
ImmutableComputableGraph code improvement + unit tests
#1042
mbabadi
opened
7 years ago
5
separate emitting from filtering based on tumor lod
#1041
davidbenjamin
closed
7 years ago
1
Prototype ADVI coverage model + germline HMM.
#1040
samuelklee
closed
7 years ago
1
Prototype siHMM.
#1039
samuelklee
closed
7 years ago
1
Prototype ADVI implementation of coverage model.
#1038
samuelklee
closed
7 years ago
5
Add warning message to add allele specific annotation group
#1037
ronlevine
closed
7 years ago
1
Use Utils methods to improve clunky code
#1036
davidbenjamin
opened
7 years ago
1
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