d1565e4e6f
Merge pull request #1261 from broadinstitute/ldg_VariantsToTableMultiallelicTypes
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Allow VariantsToTable to determine each allele's type when -SMA is used
2016-01-12 10:47:22 -05:00
593c9ddf01
Allow VariantsToTable to evaluate the type of each split variant when -F TYPE and -SMA are specified
2016-01-12 08:12:29 -05:00
7f7ba446c0
Merge pull request #1269 from broadinstitute/dr_repair_3.5_tag
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Repair the 3.5 tag in unstable
2016-01-08 16:06:33 -05:00
dc5c08f940
Repair 3.5 tag in unstable by merging the missing 3.5 commit from stable
2016-01-08 15:33:15 -05:00
d9e0b7ba58
Merge pull request #1268 from broadinstitute/ldg_fixQueueTests3
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Remove "mem_free" from resident memory request params for Queue becau…
2016-01-08 12:58:46 -05:00
204cad3646
Remove "mem_free" from resident memory request params for Queue because it doesn't work and wouldn't actually reserve memory anyway
2016-01-08 10:27:56 -05:00
f002acebdf
Merge pull request #1264 from broadinstitute/rhl_max_nocall_1262
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Backport maxNoCall functionality from GATK4
2016-01-06 14:54:24 -05:00
d16ed98c9e
Backport maxNoCall functionality from GATK4
2016-01-06 11:09:38 -05:00
1d72ab099c
Merge pull request #1247 from broadinstitute/ldg_VQSRmodelOutput
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Add optional argument for VQSR to output the model to a file as a GAT…
2016-01-05 08:35:18 -05:00
37746e40f4
Merge pull request #1263 from broadinstitute/rhl_rbp_not_merging_snps
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Merge consecutive SNPs on the same read
2016-01-04 15:37:04 -05:00
fa1d90d236
Merge consecutive SNPs on the same read
2016-01-04 13:48:59 -05:00
2ddc48914e
Add optional argument for VQSR to output the model to a file as a GATKReport
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GATKReport output also has mean and variance for annotation normalization info
2016-01-04 08:37:08 -05:00
71c6709765
Merge pull request #1145 from broadinstitute/ldg_M2_HapMapSensitivity
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Fix no-normal bug; add HapMap sensitivity benchmarking
2016-01-04 08:27:37 -05:00
4b3b5636c6
Merge pull request #1265 from broadinstitute/rhl_hc_stdout_1259
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Fix exception when writing gVCF to stdout
2015-12-29 23:07:53 -05:00
aa5e88a393
Fix exception when writing gVCF to stdout
2015-12-29 15:30:53 -05:00
7089824e1b
Merge pull request #1251 from broadinstitute/ms_annotations
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Adds new annotation, MQ of mate RankSum
2015-12-23 12:36:43 -05:00
eb6bdb2a62
MQ of Mate RankSum annotation
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Intermediate commit for tests
Adding tests
Fixing tests after rebase
Fixing one MD5
Fixing documentation
Removing annotation from standard group
Adding documentation
2015-12-23 10:24:40 -05:00
f9e9d2e273
Fix no-normal bug; add HapMap sensitivity benchmarking
2015-12-22 08:29:01 -05:00
0c3c775566
Merge pull request #1248 from broadinstitute/rhl_keep_gt
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LeftAlignAndTrimVariants --splitMultiallelics keeps GT if valid
2015-12-14 12:19:49 -05:00
9c8f035780
LeftAlignAndTrimVariants --splitMultiallelics keeps GT if valid
2015-12-14 10:42:32 -05:00
4767a83d8a
Update pom versions to mark the start of GATK 3.6 development
2015-11-25 01:52:51 -05:00
e91472ddc7
Update pom versions for the 3.5 release
2015-11-25 01:29:48 -05:00
ee63b59b52
Merge remote-tracking branch 'unstable/master'
2015-11-25 01:27:41 -05:00
9749adf22a
Merge pull request #1236 from broadinstitute/gvda_prep_M2_release_1201
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Prep MuTect2 for release
2015-11-24 20:12:57 -05:00
bf875974d1
Prep MuTect2 and ContEst for release
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Renamed M2 to MuTect2
Renamed ContaminationWalker to ContEst
Refactored related tests and usages (including in Queue scripts)
Moved M2 and ContEst + accompanying classes from private to protected
Made QSS a StandardSomaticAnnotation (new annotation group/interface) to prevent it from being sucked in with the rest of the StandardAnnotation group
2015-11-24 16:43:20 -05:00
1f8e45f0ba
Merge pull request #1243 from broadinstitute/gvda_rodwalkers_dont_downsample_1179
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Fix bug where gatkdocs of RodWalkers reported default LocusWalker downsampling settings
2015-11-23 21:39:43 -05:00
88a0514ec7
Fix bug where gatkdocs of RodWalkers reported default LocusWalker downsampling settings
2015-11-23 17:53:19 -05:00
5a3756410c
Merge pull request #1231 from broadinstitute/mf_fixBQSRIntegrationTest
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Fixes testPRWithConflictingArguments_qqAndSQQ to use -ql rather than -q1
2015-11-23 17:08:30 -05:00
b0730c2b81
Merge pull request #1239 from broadinstitute/gvda_straggler_doc_fixes_1237
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Improve doc block of GatherBqsrReports
Annotation doc enhancements (QD, InbreedingCoeff, ExcessHet and AS versions where applicable)
2015-11-22 13:58:20 -05:00
0babe6abf7
Merge pull request #1241 from broadinstitute/gvda_undeprecate_FindCoveredIntervals_1240
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Restore FindCoveredIntervals + add docs
2015-11-22 13:56:25 -05:00
a7748368f8
Yet more doc improvements prior to 3.5 release
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Improve doc block of GatherBqsrReports
Annotation doc enhancements (QD, InbreedingCoeff, ExcessHet and AS versions where applicable)
2015-11-22 10:59:24 -05:00
46ba0e519e
Restore FindCoveredIntervals + add docs
2015-11-22 10:19:04 -05:00
8f0ce02838
Merge pull request #1233 from broadinstitute/rhl_fix_example_bcf_dict
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Make the BAM header sequence dictionary match reference
2015-11-21 21:45:16 -05:00
08a9c80559
Make the header sequence dictionary match reference
2015-11-21 19:12:37 -05:00
22fa1511be
Merge pull request #1235 from broadinstitute/gvda_deprecate_useless_tools_1192
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Deprecate tools that were outdated or redundant
2015-11-21 14:58:00 -05:00
592d43f3b3
Merge pull request #1209 from broadinstitute/gvda_yet_more_doc_fixes_1195
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Many doc improvements and typo fixes
2015-11-21 02:26:46 -05:00
1cf66addaa
Deprecate tools that were outdated or redundant
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ReadAdaptorTrimmer (unsound and untested)
BaseCoverageDistribution (redundant with DiagnoseTargets)
CoveredByNSamplesSites (redundant with DiagnoseTargets)
FindCoveredIntervals (redundant with DiagnoseTargets)
VariantValidationAssessor (has a scary TODO -- REWRITE THIS TO WORK WITH VARIANT CONTEXT comment and zero tests)
LiftOverVariants, FilterLiftedVariants and liftOverVCF.pl (in #1106 ) (use Picard liftover tool)
sortByRef.pl (use Picard SortVCF)
ListAnnotations (useless)
Also deleted the java archive from the private repository (old junk we never use)
2015-11-20 22:49:40 -05:00
2570cab24c
Assorted documentation fixes, enhancements and reorganization.
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See issues referenced by the pull request for details.
2015-11-20 22:44:46 -05:00
6722ac8e8a
Merge pull request #1230 from broadinstitute/rhl_htsjdk_picard_1.141
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Rhl htsjdk picard 1.141
2015-11-20 19:47:54 -05:00
0b3b09e3ff
Move htsjdk & picard to version 1.141
2015-11-20 16:26:26 -05:00
dc0e32e3aa
Merge pull request #1223 from broadinstitute/rhl_dict_check
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Validate VCF with sequence dictionary
2015-11-20 12:43:44 -05:00
1443ee8c7f
Fixes testPRWithConflictingArguments_qqAndSQQ to use -ql rather than -q1
2015-11-20 11:23:02 -05:00
ccaddefa19
Validate VCF with sequence dictionary
2015-11-20 09:23:24 -05:00
29e86a0d01
Merge pull request #1222 from broadinstitute/yf_percent_informative_read
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Adding fraction informative reads annotation.
2015-11-18 10:08:50 -05:00
4da0d1300c
adding fraction informative reads annotation.
2015-11-18 08:39:47 -05:00
2bffe0b428
Merge pull request #1219 from broadinstitute/dr_move_GatherBqsrReports_to_protected
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Move GatherBqsrReports from private to protected
2015-11-16 22:26:54 -05:00
9d5be24778
Move GatherBqsrReports from private to protected
2015-11-10 17:40:58 -05:00
2b591d0b6f
Merge pull request #1198 from broadinstitute/ldg_moreASannotations
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Allele-specific QD and InbreedingCoeff
2015-11-10 00:35:15 -05:00
25b8ba45f4
More allele-specific annotations: AS_QD and AS_InbreedingCoeff
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Grouped default output annotations to keep them from getting dropped when -A is specified; addresses #918
Also refactored code shared by ExcessHet and InbreedingCoeff
2015-11-09 16:38:31 -05:00
fa6c1c933b
Merge pull request #1193 from broadinstitute/vrr_general_independent_af_calculator
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Added the AF independent calculator for any ploidy but seems that is no…
2015-11-07 22:14:23 -05:00
ldgauthier
Geraldine Van der Auwera
David Roazen
Ron Levine
meganshand
Mark Fleharty
Mark Fleharty
Yossi Farjoun
Yossi Farjoun
Eric Banks
Valentin Ruano Rubio