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Pull requests: broadinstitute/gatk

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Pull requests list

VAT Discrepancies [VS-1671]
#9202 opened Jun 5, 2025 by mcovarr • Draft
Bump commons-beanutils:commons-beanutils from 1.9.4 to 1.11.0 dependencies Pull requests that update a dependency file java Pull requests that update Java code
#9201 opened Jun 5, 2025 by dependabot bot Loading…
1
testing new htsjdk and picard
#9200 opened Jun 5, 2025 by lbergelson • Draft
DDO-4137 update to read artifacts from GAR
#9198 opened Jun 3, 2025 by ungwudik Loading…
4
Vs 1619
#9196 opened Jun 2, 2025 by koncheto-broad • Draft
Prep for 0.6.3 release [VS-1670]
#9194 opened May 30, 2025 by mcovarr Loading…
[DRAFT] Extend somatic support in GenotypeGVCFs to use DRAGEN SQ
#9188 opened May 27, 2025 by ldgauthier Loading…
1
Improved handling of intersecting groups in SVStratify
#9185 opened May 23, 2025 by mwalker174 Loading…
2
test yossi's fasta change
#9179 opened May 19, 2025 by lbergelson • Draft
3
Output exit result to stderr instead of stdout to allow pipelines
#9176 opened May 15, 2025 by pontushojer Loading…
1
5
Potential fix for code scanning alert no. 15: Implicit narrowing conversion in compound assignment
#9146 opened Apr 13, 2025 by lbergelson Loading…
1
Update hadoop 3.3.6 -> 3.4.0
#9132 opened Mar 28, 2025 by lbergelson Loading…
2
Add a WDL to annotate any vcf
#9122 opened Mar 22, 2025 by RoriCremer • Draft
CRAM 3.1 read support
#9095 opened Feb 11, 2025 by cmnbroad • Draft
2
Fixing what looks like a a bug in MendelianViolationEvaluator
#9080 opened Jan 15, 2025 by lbergelson Loading…
1
[DO NOT MERGE]
#9045 opened Nov 15, 2024 by jamesemery Loading…
15
Yyu test 1
#9026 opened Oct 30, 2024 by yonghaoy • Draft
Create tools for SV VCF cleaning
#8996 opened Oct 9, 2024 by kjaisingh • Draft
@kjaisingh
22
FlowFeatureMapper speed improvements
#8982 opened Sep 16, 2024 by dror27 Loading…
12
Bundle support for FeatureInputs, references; add CreateBundle tool.
#8944 opened Aug 6, 2024 by cmnbroad • Draft
7
Add keep-contig-names parameter
#8865 opened Jun 6, 2024 by gokalpcelik • Draft
3
Funcotator - removing the required transcript file
#8863 opened Jun 5, 2024 by jonn-smith • Draft
35
Changed flow allele filtering in Mutect2 to work separately on the tumor and the normal samples
#8855 opened Jun 1, 2024 by ilyasoifer • Draft
Rc vs 1365 hatcher testing parquet
#8845 opened May 23, 2024 by RoriCremer • Draft
Added long read walkers from long-running branch.
#8799 opened Apr 29, 2024 by jonn-smith Loading…
32
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