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Commits on Jun 26, 2023

• renamed VCF header

  mcovarr

  committed
  1c25535

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Commits on Jun 25, 2023

• Innocuous housekeeping changes in the partially determined haplotypes code (#8361)

  davidbenjamin

  authored
  a86d8a3

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Commits on Jun 22, 2023

• Use the correct variable when freeing github runner space: AGENT_TOOLSDIRECTORY. (#8373)

  cmnbroad

  authored
  bb22de4

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Commits on Jun 21, 2023

• Attempt to reclaim some space on the github ubuntu runner. (#8371)

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  cmnbroad

  authored
  4590e4a

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Commits on Jun 12, 2023

• Be explicit about when variants are biallelic (#8332)

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  davidbenjamin

  authored
  abe8148

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• Move to using GenomicsDB 1.5.0 (#8358)

  nalinigans

  authored
  01b30ea

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Commits on May 26, 2023

• Fixed an issue of data that contain tp tag sometimes recognized as flow (#8337)

  ilyasoifer

  authored
  4456792

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Commits on May 25, 2023

• Adding TransmittedSingleton annotation and adding quality threshold a… (#8329)

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  meganshand

  authored
  e3f30ff

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• Removing unnecessary flow based argument and option (#8342)

  ilyasoifer

  authored
  947fbce

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• Experimental tool that aligns sequencing reads to set of haplotypes / templates (#8305)

  ilyasoifer

  authored
  0ff9b91

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Commits on May 18, 2023

• Huge simplication of genotyping likelihoods calculations -- no change in output (#6351)

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  davidbenjamin

  authored
  7415882

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Commits on May 17, 2023

• Add a mergeWithRemapping() method in ReferenceConfidenceVariantContextMerger to perform allele remapping prior to genotyping (#8318)

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  droazen

  authored
  b013901

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• added tags to dockstore.yaml (#8323)

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  tmelman

  authored
  b716638

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Commits on May 16, 2023

• Matched gCNV pipeline arguments to those that were shown to have good performance in running large exome cohorts. (#8234)

  asmirnov239

  authored
  00ff83d

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Commits on May 15, 2023

• Size similarity linkage and bug fixes for SV matching tools (#8257)

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  mwalker174

  authored
  18edcd3

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Commits on May 10, 2023

• fixed typo in ReblockGVCFs arguments (#8308)

  meganshand

  authored
  642ba63

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Commits on May 3, 2023

• Adding argument to keep site level filters in ReblockGVCFs (#8304)

  meganshand

  authored
  ba483e3

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Commits on May 2, 2023

• AddFlowBaseQuality tool (#8235)

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  dror27

  and

  ilyasoifer

  authored
  d2783f7

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Commits on Apr 28, 2023

• Updated the ubuntu version for the carrot github action because github dropped support for 18.04 (#8299)

  KevinCLydon

  authored
  dd35fa9

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Commits on Apr 11, 2023

• Incorporating changes from GVS to existing files (#8256)

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  lbergelson

  authored
  0374937

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Commits on Apr 4, 2023

• Exit with code 137 when we get an OutOfMemoryError (#8277)

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  droazen

  authored
  497725a

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Commits on Apr 3, 2023

• Updates to reduce size of docker (#8259)

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  lbergelson

  authored
  bbb8be6

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Commits on Mar 30, 2023

• Updated dead link for missing reference auxiliary files message(#8273)

  jamesemery

  authored
  56693ff

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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

  authored
  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

  authored
  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
  330c59a

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