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Commits on Nov 25, 2015
  1. @vdauwera
  2. @vdauwera
  3. @vdauwera

    Merge pull request #1236 from broadinstitute/gvda_prep_M2_release_1201

    vdauwera committed Nov 24, 2015
    Prep MuTect2 for release
Commits on Nov 24, 2015
  1. @vdauwera

    Prep MuTect2 and ContEst for release

    vdauwera committed Nov 20, 2015
        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
  2. @vdauwera

    Merge pull request #1243 from broadinstitute/gvda_rodwalkers_dont_dow…

    vdauwera committed Nov 23, 2015
    …nsample_1179
    
    Fix bug where gatkdocs of RodWalkers reported default LocusWalker downsampling settings
Commits on Nov 23, 2015
  1. @vdauwera
  2. @fleharty

    Merge pull request #1231 from broadinstitute/mf_fixBQSRIntegrationTest

    fleharty committed Nov 23, 2015
    Fixes testPRWithConflictingArguments_qqAndSQQ to use -ql rather than -q1
Commits on Nov 22, 2015
  1. @vdauwera

    Merge pull request #1239 from broadinstitute/gvda_straggler_doc_fixes…

    vdauwera committed Nov 22, 2015
    …_1237
    
    Improve doc block of GatherBqsrReports
    Annotation doc enhancements (QD, InbreedingCoeff, ExcessHet and AS versions where applicable)
  2. @vdauwera

    Merge pull request #1241 from broadinstitute/gvda_undeprecate_FindCov…

    vdauwera committed Nov 22, 2015
    …eredIntervals_1240
    
    Restore FindCoveredIntervals + add docs
  3. @vdauwera

    Yet more doc improvements prior to 3.5 release

    vdauwera committed Nov 21, 2015
        Improve doc block of GatherBqsrReports
        Annotation doc enhancements (QD, InbreedingCoeff, ExcessHet and AS versions where applicable)
  4. @vdauwera
  5. @ronlevine

    Merge pull request #1233 from broadinstitute/rhl_fix_example_bcf_dict

    ronlevine committed Nov 21, 2015
    Make the BAM header sequence dictionary match reference
  6. @ronlevine
Commits on Nov 21, 2015
  1. @vdauwera

    Merge pull request #1235 from broadinstitute/gvda_deprecate_useless_t…

    vdauwera committed Nov 21, 2015
    …ools_1192
    
    Deprecate tools that were outdated or redundant
  2. @vdauwera

    Merge pull request #1209 from broadinstitute/gvda_yet_more_doc_fixes_…

    vdauwera committed Nov 21, 2015
    …1195
    
    Many doc improvements and typo fixes
  3. @vdauwera

    Deprecate tools that were outdated or redundant

    vdauwera committed Nov 20, 2015
    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)
  4. @meganshand @vdauwera

    Assorted documentation fixes, enhancements and reorganization.

    meganshand committed with vdauwera Nov 9, 2015
    See issues referenced by the pull request for details.
  5. @ronlevine

    Merge pull request #1230 from broadinstitute/rhl_htsjdk_picard_1.141

    ronlevine committed Nov 20, 2015
    Rhl htsjdk picard 1.141
Commits on Nov 20, 2015
  1. @ronlevine
  2. @ronlevine

    Merge pull request #1223 from broadinstitute/rhl_dict_check

    ronlevine committed Nov 20, 2015
    Validate VCF with sequence dictionary
  3. @fleharty
  4. @ronlevine
Commits on Nov 18, 2015
  1. @yfarjoun

    Merge pull request #1222 from broadinstitute/yf_percent_informative_read

    yfarjoun committed Nov 18, 2015
    Adding fraction informative reads annotation.
  2. @yfarjoun
Commits on Nov 17, 2015
  1. @eitanbanks

    Merge pull request #1219 from broadinstitute/dr_move_GatherBqsrReport…

    eitanbanks committed Nov 16, 2015
    …s_to_protected
    
    Move GatherBqsrReports from private to protected
Commits on Nov 10, 2015
  1. @droazen
  2. @ldgauthier

    Merge pull request #1198 from broadinstitute/ldg_moreASannotations

    ldgauthier committed Nov 10, 2015
    Allele-specific QD and InbreedingCoeff
Commits on Nov 9, 2015
  1. @ldgauthier

    More allele-specific annotations: AS_QD and AS_InbreedingCoeff

    ldgauthier committed Oct 23, 2015
    Grouped default output annotations to keep them from getting dropped when -A is specified; addresses #918
    Also refactored code shared by ExcessHet and InbreedingCoeff
Commits on Nov 8, 2015
  1. @vruano

    Merge pull request #1193 from broadinstitute/vrr_general_independent_…

    vruano committed Nov 7, 2015
    …af_calculator
    
    Added the AF independent calculator for any ploidy but seems that is no…
Commits on Nov 7, 2015
  1. @vruano

    Added the AF indepdent calculator for any ploidy but seems that is no…

    vruano committed Oct 9, 2015
    …t doing a good job for haploid
    
    Addresses issue #1078 by implementing a any-ploidy version of the independent-allele-exact-ac-calculator already available for diploids.
    
    Notice that this will change result somewhat when dealing with noisy data (low GQs).
Commits on Nov 6, 2015
  1. @fleharty

    Merge pull request #1207 from broadinstitute/mf_SV_bugfix

    fleharty committed Nov 6, 2015
    Resolves issue #1061 to use testid1 rather than testid in two integra…
  2. @fleharty
Commits on Nov 5, 2015
  1. @eitanbanks

    Merge pull request #1206 from broadinstitute/eb_suppress_alt_allele_w…

    eitanbanks committed Nov 5, 2015
    …arnings
    
    Suppress emission of the scary warning message from genotyping to no …
  2. @eitanbanks

    Suppress emission of the scary warning message from genotyping to no …

    eitanbanks committed Nov 5, 2015
    …more than once in
    
    anything but DEBUG logging mode.  Otherwise it fills up our output logs.
  3. @ldgauthier

    Merge pull request #1204 from broadinstitute/ms_fix_SelectVariants

    ldgauthier committed Nov 5, 2015
    Fix for out of date VCF version output from SelectVariants
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