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Hook up the Python-based unit tests for NVScoreVariants to our test suite
Python
tests
#9011
opened Oct 18, 2024 by
droazen
Install python-is-python3 during the GATK docker build
Docker
Python
#8497
opened Aug 25, 2023 by
droazen
ReferenceConfidenceVariantContextMerger.merge() should use remapped alleles when genotyping
bug
JointCalling
#8317
opened May 12, 2023 by
droazen
Update GATK docker base image to Ubuntu 22.04
BuildSystem
Docker
#8243
opened Mar 16, 2023 by
droazen
Funcotator feature request: custom prioritization order for mutation types
community-request
Funcotator
#7631
opened Jan 10, 2022 by
droazen
HaplotypeCaller / Mutect2 should detect amplicon data, and warn about downsampling settings
HaplotypeCaller
learn GATK
Suitable for GATK beginners
Mutect
#7567
opened Nov 15, 2021 by
droazen
IntegrationTestSpec should not ignore leading/trailing whitespace by default
learn GATK
Suitable for GATK beginners
tests
#7560
opened Nov 10, 2021 by
droazen
SelectVariants should perform site-level filtering before genotype-level filtering
learn GATK
Suitable for GATK beginners
VariantWalker
#7497
opened Oct 7, 2021 by
droazen
Auto-generated WDLs don't have localization_optional turned on
Barclay
wdl
#7094
opened Feb 22, 2021 by
droazen
Check whether outstanding GKL tickets are still valid with the latest GKL release
GKL
#7093
opened Feb 22, 2021 by
droazen
Docker build appears to be incompatible with ssh-based gatk clones
Docker
#7077
opened Feb 12, 2021 by
droazen
-ERC BP_RESOLUTION mode in HaplotypeCaller needs an integration test
HaplotypeCaller
#6833
opened Sep 17, 2020 by
droazen
Set up continuous tests for the conda environment on MacOS in Travis
tests
#6813
opened Sep 14, 2020 by
droazen
HaplotypeCaller should have (better) tests for multi-sample calling
HaplotypeCaller
tests
#6581
opened May 4, 2020 by
droazen
Uninformative error when GATK doesn't have permission to check whether a GCS bucket is Requester Pays
NIO
#6349
opened Jan 6, 2020 by
droazen
Evaluate whether we can update our jgrapht dependency to a modern version
HaplotypeCaller
#6201
opened Oct 7, 2019 by
droazen
Add additional histogram to MarkDuplicatesSpark to match Picard version
MarkDuplicatesSpark
#6155
opened Sep 11, 2019 by
droazen
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