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Potential Mismatch between the MAF output mode and VCF output mode on Gencode V43
#9013
opened Oct 18, 2024 by
jamesemery
ReVisit the PileupCaller haplotype filtering heuristics
assembly
HaplotypeCaller
Mutect
#8494
opened Aug 24, 2023 by
jamesemery
Make Functotator MafOutputRenderer agnostic to Gencode Versions
#8482
opened Aug 17, 2023 by
jamesemery
Fix mistaken string == equality comparison in GencodeFunctotation.java
bug
Funcotator
#8385
opened Jun 26, 2023 by
jamesemery
Find the source of the 5% HaplotypeCaller performance regression in the past year
HaplotypeCaller
performance
#8327
opened May 17, 2023 by
jamesemery
Unify HaplotypeCaller debugging arguments.
DRAGEN-GATK
QuixoticDream
refactoring
#8246
opened Mar 17, 2023 by
jamesemery
Add better tests and re-evaluate Pileup-Caller support for Mutect2
Mutect
QuixoticDream
#8242
opened Mar 15, 2023 by
jamesemery
Improve the commenting/warning for Forked-PR tests in Github Actions tests.
#7799
opened Apr 20, 2022 by
jamesemery
Investigate potential memory leak in GKL + HaplotypeCaller when running long intervals
HaplotypeCaller
#7693
opened Feb 23, 2022 by
jamesemery
Add better integration tests to HaplotypeCaller for less-common arguments
HaplotypeCaller
tests
#7632
opened Jan 10, 2022 by
jamesemery
Revisit "Jumbo"Annotations and find a more descriptive name
Annotations
FlowBasedGATK
HaplotypeCaller
Mutect
#7543
opened Nov 3, 2021 by
jamesemery
Capture excessive log output regressions in the test suite
QuixoticDream
tests
#7368
opened Jul 26, 2021 by
jamesemery
Add hardclip segments option to SplitNCigarReads tool
learn GATK
Suitable for GATK beginners
#7356
opened Jul 19, 2021 by
jamesemery
Reevaluate the GenotypeQuality score calculation for USE_POSTERIOR_PROBABILITIES mode
#7235
opened Apr 28, 2021 by
jamesemery
Haplotype.trim() might silently be throwing away haplotypes if the stars align
HaplotypeCaller
#7137
opened Mar 9, 2021 by
jamesemery
Add an option to DRAGEN-GATK to output PL arrays an not the prior arrays
DRAGEN-GATK
#7107
opened Feb 25, 2021 by
jamesemery
Change IOUtils.createTempFile() to be more robust to all side outputs.
Engine
enhancement
#7017
opened Jan 4, 2021 by
jamesemery
Inconsistency between Locatable.overlaps() and SimpleInterval.Overlaps() methods
bug
HTSJDK
#6898
opened Oct 16, 2020 by
jamesemery
Fix FragmentUtils.adjustQualsOfOverlappingPairedFragments() to better handle indels
HaplotypeCaller
Mutect
#6890
opened Oct 15, 2020 by
jamesemery
Investigate issues in reads realignment results for DRAGEN-GATK
DRAGEN-GATK
HaplotypeCaller
#6706
opened Jul 16, 2020 by
jamesemery
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