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Commits on Jun 4, 2024

• Permutect dataset engine outputs contig and read group indices, not names (broadinstitute#8860)

  davidbenjamin

  authored
  2a420e4

• Mutect2 WDL and GetSampleName can handle multiple sample names in BAM headers (broadinstitute#8859)

  davidbenjamin

  authored
  2878ce5

Commits on Jun 3, 2024

• Mutect2 germline resource can have split multiallelic format (broadinstitute#8837)

  davidbenjamin

  authored
  0be44f2

• [BIOIN-1570] Fixed edge case in variant annotation (broadinstitute#8810)

  Show description for d4744f7
  ilyasoifer

  authored
  d4744f7

Commits on May 17, 2024

• Bigger Permutect tensors and Permutect test datasets can be annotated with truth VCF (broadinstitute#8836)

  Show description for 4ed93fe
  davidbenjamin

  authored
  4ed93fe

Commits on May 15, 2024

• VariantFiltration: added arg to write custom mask filter description in VCF header (broadinstitute#8831)

  Show description for a3bbfc4
  meganshand

  authored
  a3bbfc4

Commits on May 9, 2024

• Reduced docker layers in GATK image from 44 to 16 (broadinstitute#8808)

  Show description for c6daf7d
  kevinpalis

  authored
  c6daf7d

Commits on May 6, 2024

• Allow for GT to be a nocall if GQ and PL[0] are zero instead of homref in GenomicsDB (broadinstitute#8759)

  Show description for 24f93b5
  

  nalinigans

  and

  Nalini Ganapati

  authored
  24f93b5

Commits on May 2, 2024

• Bug fix in flow allele filtering (broadinstitute#8775)

  Show description for 5c32785
  ilyasoifer

  authored
  5c32785

Commits on May 1, 2024

• Add malaria spanning deletion exception regression test with fix (broadinstitute#8802)

  Show description for ec39c37
  

  ldgauthier

  and

  jonn-smith

  authored
  ec39c37

Commits on Apr 18, 2024

• Gc getpipeupsummaries use mappingqualityreadfilter (broadinstitute#8781)

  Show description for aed8b1b
  gokalpcelik

  authored
  aed8b1b

Commits on Apr 12, 2024

• Enable ReblockGVCF to subset AS annotations that aren't "raw" (pipe-delimited) (broadinstitute#8771)

  Show description for 986cb15
  ldgauthier

  authored
  986cb15

Commits on Apr 11, 2024

• Re-commit large files as lfs stubs (broadinstitute#8769)

  Show description for 47c4858
  lbergelson

  authored
  47c4858

Commits on Apr 10, 2024

• Several GQ0 cleanup changes: (broadinstitute#8741)

  Show description for 7cdc985
  ldgauthier

  authored
  7cdc985

Commits on Apr 4, 2024

• SNVQ recalibration tool added for flow based reads (broadinstitute#8697)

  Show description for 6739e6d
  

  ilyasoifer

  and

  Dror Kessler

  authored
  6739e6d

Commits on Apr 1, 2024

• Funcotator: suppress a log message about b37 contigs when not doing b37/hg19 conversion (broadinstitute#8758)

  Show description for 724b5bc
  droazen

  authored
  724b5bc

Commits on Mar 25, 2024

• Make M2 haplotype and clustered events filters smarter about germline events (broadinstitute#8717)

  Show description for 105b63e
  davidbenjamin

  authored
  105b63e

Commits on Mar 20, 2024

• Now we should be excluding the test folder from code coverage calculations (broadinstitute#8744)

  KevinCLydon

  authored
  47a97ae

Commits on Mar 19, 2024

• Update README to include list of popular software included in docker image (broadinstitute#8745)

  Show description for dcfaa06
  rickymagner

  authored
  dcfaa06

Commits on Mar 18, 2024

• dragstr model in Mutect2 WDL (broadinstitute#8716)

  davidbenjamin

  authored
  141529b

Commits on Mar 12, 2024

• Fix to long deletions that overhang into the assembly window causing exceptions in HaplotypeCaller (broadinstitute#8731)

  jamesemery

  authored
  8ee86e7

Commits on Mar 11, 2024

• GatherVcfsCloud is no longer beta (broadinstitute#8680)

  lbergelson

  authored
  2640404

• added --inverted-read-filter argument to allow for selecting reads that fail read filters from the command line easily (broadinstitute#8724)

  jamesemery

  authored
  b81a638

• Improve failure message in VariantContextTestUtils (broadinstitute#8725)

  lbergelson

  authored
  9af1be3

Commits on Mar 8, 2024

• Update the setup_cloud github action (broadinstitute#8651)

  Show description for c3599a0
  lbergelson

  authored
  c3599a0

Commits on Mar 7, 2024

• fix no data hom refs (broadinstitute#8715)

  Show description for b0463e4
  ldgauthier

  authored
  b0463e4

• Standardize test results directory between normal/docker tests (broadinstitute#8718)

  Show description for a2ebb37
  lbergelson

  authored
  a2ebb37

Commits on Mar 5, 2024

• Move to GenomicsDB 1.5.2 which supports M1 macs (broadinstitute#8710)

  Show description for c97faf6
  nalinigans

  authored
  c97faf6

Commits on Feb 15, 2024

• Handle CTX_INV subtype in SVAnnotate (broadinstitute#8693)

  epiercehoffman

  authored
  cfd4d87

Commits on Feb 7, 2024

• Parameterize the logging frequency for ProgressLogger in GatherVcfsCloud. (broadinstitute#8662)

  gbggrant

  authored
  bbc028b

Commits on Jan 30, 2024

• normal artifact lod is now defined without the extra minus sign (broadinstitute#8668)

  davidbenjamin

  authored
  dd73036

Commits on Jan 26, 2024

• Improvements to Mutect2's Permutect training data mode (broadinstitute#8663)

  Show description for 2d50cf8
  davidbenjamin

  authored
  2d50cf8

Commits on Jan 23, 2024

• Rewrite complex SV functional annotation in SVAnnotate (broadinstitute#8516)

  epiercehoffman

  authored
  e796d20

Commits on Dec 14, 2023

• Reduce SVConcordance memory footprint (broadinstitute#8623)

  mwalker174

  authored
  b68fadc

• Output the new image name at the end of a successful cloud docker build (broadinstitute#8627)

  droazen

  authored
  39cfbba

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