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Commits on Mar 29, 2023

• Remove spurious flags from beloved argument (#8271)

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  jamesemery

  authored
  42fccfc

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• Better Gnarly error message (#8270)

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  ldgauthier

  authored
  ef860bf

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Commits on Mar 28, 2023

• Added resource usage section to the GermlineCNVCaller java doc. (#8064)

  asmirnov239

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  4dc8e2a

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Commits on Mar 23, 2023

• Fix warnings in Github Actions (#8241)

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  lbergelson

  authored
  148dd33

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Commits on Mar 21, 2023

• Metrics documentation generation. (#7749)

  cmnbroad

  authored
  b370c06

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• Checkpoint of necessary changes for DRAGEN v3.7.8 concordance (#8083)

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  jamesemery

  authored
  9afa998

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• Use sample set intersection for SVConcordance (#8211)

  mwalker174

  authored
  e68f066

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• Incorporate build.gradle changes from gvs (#8249)

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  lbergelson

  authored
  2bda7f9

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Commits on Mar 16, 2023

• Added documentation on OMP_NUM_THREADS and MKL_NUM_THREADS to GermlineCNVCaller and DetermineGermlineContigPloidy. (#8223)

  samuelklee

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  2dbc025

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Commits on Mar 15, 2023

• Update base image to 3.0.0(#8228)

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  lbergelson

  authored
  bab0adc

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Commits on Mar 7, 2023

• FlowFeatureMapper: added surrounding-median-quality-size feature (#8222)

  dror27

  authored
  4ba4ab5

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Commits on Mar 2, 2023

• Move to Java 17! (#8035)

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  3 peopleauthored
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• removing A,R, and G length attributes when ReblockGVCF subsets an allele (#8209)

  meganshand

  authored
  4c1fb92

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Commits on Feb 28, 2023

• Modified VariantRecalibrator to only use a deduped annotations list. This resolves issues that can result from differences in the number of annotations in the original and deduped lists. Also fixed…

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  KevinCLydon

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  227bbca

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• Deprecate some args (#8140)

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  ldgauthier

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Commits on Feb 23, 2023

• add error message for when tree-score-threshold is set in ReblockGVCF… (#8218)

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  meganshand

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  24f62de

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Commits on Feb 22, 2023

• Added scattered gcnv case wdl to dockstore file (#8217)

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  tmelman

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  3e9a316

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Commits on Feb 21, 2023

• Fixing a bug in parsing of T0 tag (#8185)

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  ilyasoifer

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  b4682ba

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Commits on Feb 15, 2023

• Enabled GVCF type filtering support in SelectVariants (#7193)

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  michaelgatzen

  authored
  692e7a3

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• Allow empty input in TransferReadTags (#8198)

  kachulis

  authored
  a88ac4e

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Commits on Feb 14, 2023

• Prevent close from hiding causal exceptions #528 (#7764)

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  lbergelson

  authored
  f7dea3c

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Commits on Feb 9, 2023

• Updated M2 parameters to make them consistent with HC (#8186)

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  ilyasoifer

  authored
  b7f24ff

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• Implement SVConcordance tool (#7977)

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  mwalker174

  authored
  d3b2c5c

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Commits on Feb 6, 2023

• Fixed gCNV bug that breaks the inference when only 2 intervals are provided. (#8180)

  asmirnov239

  authored
  110f4f5

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Commits on Feb 1, 2023

• Make several Funcotator methods and fields protected so it is easiest to extend the tool (#8166)

  bbimber

  authored
  d1a4f94

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Commits on Jan 28, 2023

• bug in dynamic read disqualification fixed (#8171)

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  ilyasoifer

  authored
  a3c1d2c

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Commits on Jan 12, 2023

• Fix NPE from unintialized logger in GenotypingEngine (#8159)

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  lbergelson

  authored
  43e2d04

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Commits on Jan 7, 2023

• SelectVariants JEXL filter fixes and refactor (#8092)

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  takutosato

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Commits on Jan 5, 2023

• minor documentation fix (#8145)

  jamesemery

  authored
  9ced727

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Commits on Jan 3, 2023

• Recognize MEI DELs with ALT format <DEL:ME> in SVAnnotate (#8125)

  epiercehoffman

  authored
  3687415

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Commits on Dec 24, 2022

• Removed commented lines from somatic CNV WDL. (#8130)

  samuelklee

  authored
  0261d43

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• Replace File.createTempFile with IOUtils.createTempFile (#6780)

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  lbergelson

  authored
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Commits on Dec 23, 2022

• Improvements to PileupDetectionArgumentCollection documentation (#8050)

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  Yossi Farjoun

  authored
  16fc4f1

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• removed two ancient and unused test files that are probably no-longer needed (#7634)

  jamesemery

  authored
  4e97a8b

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• Add GenomicsDBArgumentCollection to CreateSomaticPanelOfNormals tool (#6746)

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  nalinigans

  authored
  9ffd649

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