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Commits on Oct 24, 2024

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

  Show description for 02c87bf
  lbergelson

  authored
  02c87bf

Commits on Oct 23, 2024

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

  Show description for dffedfb
  lbergelson

  authored
  dffedfb

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

  Show description for c4860d4
  jamesemery

  authored
  c4860d4

• Additional Dependency updates (#9006)

  Show description for d056c32
  lbergelson

  authored
  d056c32

Commits on Oct 18, 2024

• Mark NVScoreVariants as a beta feature (#9010)

  droazen

  authored
  b409f77

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

  Show description for d6acb84
  droazen

  authored
  d6acb84

• Update gradle and build.gradle (#8998)

  Show description for df8e4b7
  lbergelson

  authored
  df8e4b7

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

  KevinCLydon

  authored
  c18f3e2

• Update docker base (#9005)

  Show description for 07eac31
  lbergelson

  authored
  07eac31

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

  Show description for f5a2256
  

  gokalpcelik

  and

  lbergelson

  authored
  f5a2256

Commits on Oct 17, 2024

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

  jamesemery

  authored
  87e9f1f

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

  Show description for a377b07
  

  droazen

  and

  lbergelson

  authored
  a377b07

Commits on Oct 16, 2024

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

  Show description for a070efc
  droazen

  authored
  a070efc

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

  Show description for 779489b
  lbergelson

  authored
  779489b

Commits on Oct 14, 2024

• Update Mutect2.java Documentation (#8999)

  Show description for fa3f11c
  gokalpcelik

  authored
  fa3f11c

Commits on Sep 27, 2024

• Updates to VcfComparator (#8973)

  Show description for 2e459a5
  meganshand

  authored
  2e459a5

Commits on Sep 25, 2024

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

  Show description for 3401a33
  nalinigans

  authored
  3401a33

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

Commits on Sep 18, 2024

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

  Show description for 6036d67
  

  lbergelson

  and

  jamesemery

  authored
  6036d67

Commits on Sep 12, 2024

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

  Show description for 2ba3a15
  meganshand

  authored
  2ba3a15

Commits on Sep 11, 2024

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

  mwalker174

  authored
  6bb5217

Commits on Sep 4, 2024

• Update detector output files. (#8971)

  Show description for 1258174
  cmnbroad

  authored
  1258174

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

  cmnbroad

  authored
  f42b7f7

Commits on Aug 29, 2024

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

  Show description for 3c1430d
  sanashah007

  authored
  3c1430d

Commits on Aug 9, 2024

• Add docs about citing GATK (#8947)

  rickymagner

  authored
  9f2fbb5

Commits on Aug 6, 2024

• Adds VcfComparator tool (#8933)

  Show description for 096be07
  

  meganshand

  and

  ldgauthier

  authored
  096be07

Commits on Jul 30, 2024

• adding test to match WARP tests edge case (#8928)

  meganshand

  authored
  64dc4b3

Commits on Jul 25, 2024

• X_FILTERED_COUNT semantics adjusted in FlowFeatureMapper (#8894)

  dror27

  authored
  3d99f22

Commits on Jul 24, 2024

• Modified HaplotypeBasedVariantRecaller to support non-flow reads (#8896)

  ilyasoifer

  authored
  747df1a

Commits on Jul 12, 2024

• Clarify in the README which git lfs files are required to build GATK (#8914)

  Show description for 59c9c1b
  droazen

  authored
  59c9c1b

• Update hdf5-java-bindings to version 1.2.0-hdf5_2.11.0, which removes log4j 1.x (#8908)

  droazen

  authored
  b97448c

Commits on Jul 11, 2024

• Complex SV intervals support (#8521)

  Show description for 23a38ce
  mwalker174

  authored
  23a38ce

Commits on Jul 9, 2024

• Updated Python and PyMC, removed TensorFlow, and added PyTorch in conda environment. (#8561)

  Show description for ddaf66f
  samuelklee

  authored
  ddaf66f

Commits on Jul 1, 2024

• Handle CTX_PP/QQ and CTX_PQ/QP CPX_TYPE values in SVConcordance (#8885)

  epiercehoffman

  authored
  4af2b49

Commits on Jun 29, 2024

• Update HTSJDK to 4.1.1 and Picard to 3.2.0 (#8900)

  Show description for 64348bc
  droazen

  authored
  64348bc

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