Skip to content
Commits on Nov 25, 2015
  1. @vdauwera
  2. @vdauwera
  3. @vdauwera
Commits on Nov 24, 2015
  1. @vdauwera

    Prep MuTect2 and ContEst for release

    vdauwera committed
        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
    …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
    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
    …_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
    …eredIntervals_1240
    
    Restore FindCoveredIntervals + add docs
  3. @vdauwera

    Yet more doc improvements prior to 3.5 release

    vdauwera committed
        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
    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
    …ools_1192
    
    Deprecate tools that were outdated or redundant
  2. @vdauwera

    Merge pull request #1209 from broadinstitute/gvda_yet_more_doc_fixes_…

    vdauwera committed
    …1195
    
    Many doc improvements and typo fixes
  3. @vdauwera

    Deprecate tools that were outdated or redundant

    vdauwera committed
    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
    See issues referenced by the pull request for details.
  5. @ronlevine
Commits on Nov 20, 2015
  1. @ronlevine
  2. @ronlevine

    Merge pull request #1223 from broadinstitute/rhl_dict_check

    ronlevine committed
    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
    Adding fraction informative reads annotation.
  2. adding fraction informative reads annotation.

    Yossi Farjoun committed
Commits on Nov 17, 2015
  1. @eitanbanks

    Merge pull request #1219 from broadinstitute/dr_move_GatherBqsrReport…

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

    More allele-specific annotations: AS_QD and AS_InbreedingCoeff

    ldgauthier committed
    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
    …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
    …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
    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
    …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
    …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
    Fix for out of date VCF version output from SelectVariants
Something went wrong with that request. Please try again.