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Pull requests: broadinstitute/gatk

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Pull requests list

Plumb through train_extra_args to allow bypass of INDEL training
#9276 opened Sep 26, 2025 by mcovarr Loading…
Bump org.apache.zookeeper:zookeeper from 3.9.2 to 3.9.4 dependencies Pull requests that update a dependency file java Pull requests that update Java code
#9274 opened Sep 24, 2025 by dependabot bot Loading…
Accurately index outputs from PrintSVEvidence and CollectSVEvidence
#9269 opened Sep 22, 2025 by kjaisingh Loading…
Hatcher testing parquet
#9267 opened Sep 19, 2025 by koncheto-broad • Draft
Update MendelianViolation . Fix java.lang.IndexOutOfBoundsException: when a genotype is haploid.
#9241 opened Jul 30, 2025 by lindenb Loading…
Ploidy status rows
#9229 opened Jul 15, 2025 by mcovarr • Draft
Bump org.apache.commons:commons-lang3 from 3.14.0 to 3.18.0 dependencies Pull requests that update a dependency file java Pull requests that update Java code
#9224 opened Jul 12, 2025 by dependabot bot Loading…
Bump com.nimbusds:nimbus-jose-jwt from 9.41.2 to 10.0.2 dependencies Pull requests that update a dependency file java Pull requests that update Java code
#9223 opened Jul 11, 2025 by dependabot bot Loading…
BQSR: restore ability to specify custom covariates and to disable standard covariates. (Take 2)
#9206 opened Jun 12, 2025 by takutosato Loading…
44
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 Loading…
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
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