Commits

Branch selector

 master

User selector

ldgauthier

Datepicker

All time

Commit History

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

  Copy full SHA for ec39c37

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

  Copy full SHA for 986cb15

Commits on Apr 10, 2024

• Several GQ0 cleanup changes: (broadinstitute#8741)

  Show description for 7cdc985
  ldgauthier

  authored
  7cdc985

  Copy full SHA for 7cdc985

Commits on Mar 7, 2024

• fix no data hom refs (broadinstitute#8715)

  Show description for b0463e4
  ldgauthier

  authored
  b0463e4

  Copy full SHA for b0463e4

Commits on Aug 14, 2023

• mutect2 expose param (broadinstitute#8447)

  Show description for 9e0e1ff
  ldgauthier

  authored
  9e0e1ff

  Copy full SHA for 9e0e1ff

Commits on Jul 17, 2023

• Add haploid support to GnarlyGenotyper (broadinstitute#7750)

  ldgauthier

  authored
  7d900f5

  Copy full SHA for 7d900f5

Commits on Mar 29, 2023

• Better Gnarly error message (broadinstitute#8270)

  Show description for ef860bf
  ldgauthier

  authored
  ef860bf

  Copy full SHA for ef860bf

Commits on Feb 28, 2023

• Deprecate some args (broadinstitute#8140)

  Show description for 6b2440d
  ldgauthier

  authored
  6b2440d

  Copy full SHA for 6b2440d

Commits on Jun 17, 2022

• Type change int -> long to prevent tranche novel variant count overflow (broadinstitute#7864)

  Show description for add34e1
  ldgauthier

  authored
  add34e1

  Copy full SHA for add34e1

Commits on May 11, 2022

• Docs clarification for some reblocking-related funkiness (broadinstitute#7846)

  ldgauthier

  authored
  72684d0

  Copy full SHA for 72684d0

Commits on Apr 12, 2022

• Remove bad "safety check" in GGVCFs (broadinstitute#7772)

  Show description for 33bda5e
  ldgauthier

  authored
  33bda5e

  Copy full SHA for 33bda5e

Commits on Mar 30, 2022

• Fix for NPE when GDB has too many alleles (broadinstitute#7738)

  Show description for a85c25f
  ldgauthier

  authored
  a85c25f

  Copy full SHA for a85c25f

Commits on Mar 10, 2022

• Docs correction for the --heterozygosity argument in the GenotypeCalculationArgumentCollection (broadinstitute#7661)

  Show description for 572b84a
  ldgauthier

  authored
  572b84a

  Copy full SHA for 572b84a

Commits on Mar 8, 2022

• Revert AF calculation bug and yet another reblocking fix (broadinstitute#7670)

  Show description for 2d2cca2
  ldgauthier

  authored
  2d2cca2

  Copy full SHA for 2d2cca2

Commits on Feb 4, 2022

• Add new max alt argument for GenomicsDB and require it to be >= GGVCFs (broadinstitute#7655)

  ldgauthier

  authored
  da7cd83

  Copy full SHA for da7cd83

Commits on Jan 31, 2022

• Fix case where hom-ref "variant" with no data had wrong sized PLs and (broadinstitute#7644)

  Show description for d373a50
  ldgauthier

  authored
  d373a50

  Copy full SHA for d373a50

Commits on Dec 21, 2021

• Fix developer doc in AS_RMSMappingQuality (broadinstitute#7607)

  ldgauthier

  authored
  a799ce9

  Copy full SHA for a799ce9

Commits on Oct 29, 2021

• Fix annotation NPE when there are no informative reads (broadinstitute#7186)

  Show description for cddd336
  ldgauthier

  authored
  cddd336

  Copy full SHA for cddd336

Commits on Oct 6, 2021

• Fix GenotypeGVCFs bug for variants with zero or no INFO DP (broadinstitute#7491)

  Show description for ec514b7
  ldgauthier

  authored
  ec514b7

  Copy full SHA for ec514b7

Commits on Sep 25, 2021

• Improve consistency for heterozygosity annotations on reblocked inputs (broadinstitute#7471)

  Show description for c1f3737
  ldgauthier

  authored
  c1f3737

  Copy full SHA for c1f3737

Commits on Sep 2, 2021

• GenotypeGVCFs update for reblocked GVCFs (broadinstitute#7223)

  Show description for 24a8e02
  ldgauthier

  authored
  24a8e02

  Copy full SHA for 24a8e02

Commits on Aug 18, 2021

• ReblockGVCF is now out of beta (broadinstitute#7419)

  Show description for cafc6ce
  ldgauthier

  authored
  cafc6ce

  Copy full SHA for cafc6ce

Commits on Aug 17, 2021

• Update annotation args to GATK4 names (broadinstitute#7413)

  ldgauthier

  authored
  b912fad

  Copy full SHA for b912fad

Commits on Aug 13, 2021

• Check that GVCF ref blocks don't overlap (broadinstitute#7405)

  Show description for f339e1c
  ldgauthier

  authored
  f339e1c

  Copy full SHA for f339e1c

• Address reblocking empty buffer cases and off-by-one at contig starts (broadinstitute#7404)

  Show description for 6d9fa5b
  ldgauthier

  authored
  6d9fa5b

  Copy full SHA for 6d9fa5b

Commits on Aug 10, 2021

• Two ReblockGVCF fixes (broadinstitute#7400)

  Show description for 1ef446e
  ldgauthier

  authored
  1ef446e

  Copy full SHA for 1ef446e

Commits on Aug 4, 2021

• Updated GVCF "reblocking" with no gaps, no overlaps (broadinstitute#7122)

  Show description for 68710b4
  ldgauthier

  authored
  68710b4

  Copy full SHA for 68710b4

Commits on Aug 3, 2021

• comment fix in MultiVariantDataSource.java (broadinstitute#7388)

  Show description for 796af9f
  ldgauthier

  authored
  796af9f

  Copy full SHA for 796af9f

Commits on May 13, 2021

• Clarify Gnarly pipeline inputs (broadinstitute#7231)

  Show description for ef67551
  ldgauthier

  authored
  ef67551

  Copy full SHA for ef67551

Commits on Jan 29, 2021

• Nothing is ever easy

  ldgauthier

  committed
  9ff3f8b

  Copy full SHA for 9ff3f8b

• Update old docs with GATK4 name: ApplyRecalibration -> ApplyVQSR

  ldgauthier

  committed
  afa5319

  Copy full SHA for afa5319

Commits on Jan 12, 2021

• Add locus info to ref allele mismatch exception (broadinstitute#6964)

  ldgauthier

  authored
  b1aab93

  Copy full SHA for b1aab93

Commits on Dec 23, 2020

• gCNV joint calling improvements:

  Show description for 31df35b
  ldgauthier

  committed
  31df35b

  Copy full SHA for 31df35b

Commits on Dec 4, 2020

• Ensure CalculateGenotypePosteriors resources have same sequence dictionary as input VCF (broadinstitute#6430)

  ldgauthier

  authored
  956fc0d

  Copy full SHA for 956fc0d

• Fix AS annotation warning args from GATK3 names to GATK4 names (broadinstitute#6985)

  ldgauthier

  authored
  01be4ca

  Copy full SHA for 01be4ca

Pagination

Previous

Next