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Commits on Nov 9, 2017

• Update pom versions for the 3.8-1 release

  

  Geraldine Van der Auwera

  committed
  41147a6

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• Merge remote-tracking branch 'unstable/master'

  

  Geraldine Van der Auwera

  committed
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• Update pom versions to mark the start of GATK 3.9 development

  

  Geraldine Van der Auwera

  committed
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Commits on Oct 24, 2017

• Serialized GMM no longer depends on command line annotation order (#1632)

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  lucidtronix

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Commits on Sep 30, 2017

• Upgrade GKL to 0.6.0 (#1631)

  

  erniebrau

  authored and

  Geraldine Van der Auwera

  committed
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Commits on Sep 6, 2017

• Update GKL to 0.5.9 (#1629)

  

  erniebrau

  authored and

  Geraldine Van der Auwera

  committed
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Commits on Aug 29, 2017

• Revert "Changed GKL version to 0.5.6 (#1626)" (#1628)

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  Geraldine Van der Auwera

  authored
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• Changed GKL version to 0.5.6 (#1626)

  

  erniebrau

  authored and

  Geraldine Van der Auwera

  committed
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Commits on Aug 19, 2017

• Change to GKL 0.5.5, which fixes a bug in FPGA 'private' mode (#1623)

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  erniebrau

  authored and

  Geraldine Van der Auwera

  committed
  0beac9b

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Commits on Aug 7, 2017

• Merge pull request #1622 from broadinstitute/rhl_vtt_fix_doc_typos

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  Geraldine Van der Auwera

  authored
  dd1c237

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• Merge pull request #1625 from broadinstitute/ldg_fixPLsubsettingGQproblem

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  Geraldine Van der Auwera

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Commits on Aug 4, 2017

• Update the GQ after PLs get subset

  ldgauthier

  committed
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Commits on Jul 29, 2017

• Fix VariantsToTable documentation typos

  ronlevine

  committed
  099f772

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Commits on Jul 28, 2017

• Update pom versions to mark the start of GATK 3.9 development

  

  Geraldine Van der Auwera

  committed
  a50aeb3

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• Update pom versions for the 3.8 release

  

  Geraldine Van der Auwera

  committed
  1f5b68b

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• Merge remote-tracking branch 'unstable/master'

  

  Geraldine Van der Auwera

  committed
  ebc824e

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• Merge pull request #1621 from broadinstitute/gvda_clean_slate

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  Geraldine Van der Auwera

  authored
  e4764d3

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• Update release scripts

  

  Geraldine Van der Auwera

  committed
  827c719

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• Updated gatkdocs template

  

  Geraldine Van der Auwera

  committed
  92d11cc

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• Fix problem filename

  

  Geraldine Van der Auwera

  committed
  a7d8478

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Commits on Jul 24, 2017

• Merge pull request #1615 from broadinstitute/gvda_archive_docs

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  Geraldine Van der Auwera

  authored
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Commits on Jul 23, 2017

• Archive GATK3-specific docs from the forum

  

  Geraldine Van der Auwera

  committed
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• Merge pull request #1609 from broadinstitute/yf_make_readutils_test_public

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  Geraldine Van der Auwera

  authored
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Commits on Jul 21, 2017

• Make error informative for non-diploid family likelihoods

  ronlevine

  committed
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Commits on Jul 18, 2017

• Move htsjdk to ver 2.10.1 and picard to ver 2.10.2

  ronlevine

  committed
  0ec0081

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• Merge pull request #1610 from broadinstitute/ldg_fixRankSumHistogramOutput2

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  ldgauthier

  authored
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• Changed ASRankSum single-sample output so it's combine-able

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  ldgauthier

  committed
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Commits on Jun 30, 2017

• Merge pull request #1608 from broadinstitute/ldg_renomalizeVQSRdata

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  ldgauthier

  authored
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• Normalize input data by same annotation normalization scheme as input model

  ldgauthier

  committed
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Commits on Jun 28, 2017

• - responding to reviewer's comments.

  yfarjoun

  committed
  8348d29

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• Deprecate --allowMissingData, add --errorIfMissingData and print NA for null object in VariantsToTable

  ronlevine

  committed
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Commits on Jun 27, 2017

• Merge pull request #1605 from broadinstitute/ldg_updateReference

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  ldgauthier

  authored
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Commits on Jun 26, 2017

• Update all the md5s for header reference path changes

  ldgauthier

  committed
  b81a02d

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• Merge pull request #1604 from broadinstitute/rhl_close_printstream_1600

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  ldgauthier

  authored
  4f2f62f

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• Close BQSRGatherer's PrintStream when finished

  ronlevine

  committed
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