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Commits on Jan 16, 2025

• Remove unecessary calculation and methods in FlowBasedRead (#9077)

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  lbergelson

  authored
  717d8a9

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• Bump ch.qos.logback:logback-core from 1.4.14 to 1.5.13 (#9079)

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  dependabot[bot]

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  lbergelson

  authored
  c819ff6

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Commits on Jan 15, 2025

• Close a FeatureReader after use in HaplotypeCallerEngine (#9078)

  lbergelson

  authored
  373df45

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Commits on Dec 10, 2024

• Updating upload_artifact in github actions (#9061)

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  lbergelson

  authored
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Commits on Dec 3, 2024

• Prioritize het calls when merging clustered SVs (#9058)

  mwalker174

  authored
  fc248df

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Commits on Nov 19, 2024

• Update README.md (#9047)

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  gokalpcelik

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  lbergelson

  authored
  cf88d08

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Commits on Nov 18, 2024

• VariantRecalibrator R script fix for recent R versions. (#9046)

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  gokalpcelik

  authored
  f7faad9

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• Add SVStratify and GroupedSVCluster tools (#8990)

  mwalker174

  authored
  3bb2b8b

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Commits on Nov 13, 2024

• Retain all source IDs on VariantContext (#9032)

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  bbimber

  and

  lbergelson

  authored
  18707c6

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Commits on Nov 8, 2024

• Port of CallableLoci from GATK3 (#9031)

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  jonn-smith

  authored
  3fe011a

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Commits on Oct 24, 2024

• Change the kryo version specification to use maven style [,) instead of + (#9018)

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  lbergelson

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  02c87bf

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Commits on Oct 23, 2024

• Use jetty bom to enforce uniform jetty versions (#9016)

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  lbergelson

  authored
  dffedfb

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• Added a '--prefer-mane-transcripts' mode that enforces MANE_Select tagged Gencode transcripts where possible (#9012)

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  jamesemery

  authored
  c4860d4

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• Additional Dependency updates (#9006)

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  lbergelson

  authored
  d056c32

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Commits on Oct 18, 2024

• Mark NVScoreVariants as a beta feature (#9010)

  droazen

  authored
  b409f77

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• Remove CNNScoreVariants, CNNVariantTrain, and CNNVariantWriteTensors (#9009)

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  droazen

  authored
  d6acb84

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• Update gradle and build.gradle (#8998)

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  lbergelson

  authored
  df8e4b7

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• Added a check for whether files can be created and executed within the configured tmp-dir (#8951)

  KevinCLydon

  authored
  c18f3e2

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• Update docker base (#9005)

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  lbergelson

  authored
  07eac31

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• Adding small warning messages to not to feed any GVCF files to these tools (#9008)

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  gokalpcelik

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  lbergelson

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  f5a2256

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Commits on Oct 17, 2024

• Re-added --only-output-calls-starting-in-intervals as a deprecated argument. (#9000)

  jamesemery

  authored
  87e9f1f

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• Port of nvscorevariants into GATK, with a basic tool frontend (#8004)

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  droazen

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  lbergelson

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  a377b07

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Commits on Oct 16, 2024

• Add more detailed conda setup instructions to the GATK README (#9001)

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  droazen

  authored
  a070efc

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• Add dependency submission workflow to monitor vulnerabilities (#9002)

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  lbergelson

  authored
  779489b

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Commits on Oct 14, 2024

• Update Mutect2.java Documentation (#8999)

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  gokalpcelik

  authored
  fa3f11c

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Commits on Sep 27, 2024

• Updates to VcfComparator (#8973)

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  meganshand

  authored
  2e459a5

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Commits on Sep 25, 2024

• Warn instead of throwing when querying intervals that were not in GenomicsDBImport (#8987)

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  nalinigans

  authored
  3401a33

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Commits on Sep 24, 2024

• Swapped mito mode in Mutect to use the mode argument utils, providing better override behavior and documentation (#8986)

  jamesemery

  authored
  e1b5f95

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Commits on Sep 18, 2024

• Added new argument "--variant-output-filtering" to variant walkers for customized filtering of output variants to intervals. (#6388)

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  lbergelson

  and

  jamesemery

  authored
  6036d67

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Commits on Sep 12, 2024

• Adds QD and AS_QD emission from VariantAnnotator on GVS input (#8978)

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  meganshand

  authored
  2ba3a15

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Commits on Sep 11, 2024

• Require both overlap and breakend proximity for depth-only SV clustering (#8962)

  mwalker174

  authored
  6bb5217

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Commits on Sep 4, 2024

• Update detector output files. (#8971)

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  cmnbroad

  authored
  1258174

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• Update the large test CRAM files to CRAM v3.0. (#8832)

  cmnbroad

  authored
  f42b7f7

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Commits on Aug 29, 2024

• Issue #7159 Create tool for producing genomic regions (as a BED file) (#8942)

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  sanashah007

  authored
  3c1430d

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Commits on Aug 9, 2024

• Add docs about citing GATK (#8947)

  rickymagner

  authored
  9f2fbb5

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