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Pull requests: broadinstitute/gatk

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Pull requests list

Vs 1611 - herding cats
#9118 opened Mar 12, 2025 by koncheto-broad • Draft
1
Extract memory footprint part I [VS-1590]
#9116 opened Mar 10, 2025 by mcovarr Loading…
@RoriCremer @koncheto-broad
2
Extract avros for a VDS but only include the NEW samples that are in Foxtrot
#9105 opened Mar 3, 2025 by RoriCremer Loading…
6
CRAM 3.1 read support
#9095 opened Feb 11, 2025 by cmnbroad • Draft
Add samtools for file format testing.
#9093 opened Feb 10, 2025 by cmnbroad • Draft
2
Fixing what looks like a a bug in MendelianViolationEvaluator
#9080 opened Jan 15, 2025 by lbergelson Loading…
1
Add VAT clinvar reverse complement
#9070 opened Jan 7, 2025 by RoriCremer Loading…
8
[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 • Draft
12
Bundle support for FeatureInputs, references; add CreateBundle tool.
#8944 opened Aug 6, 2024 by cmnbroad • Draft
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
add echocallset as an option for integration test
#8757 opened Apr 1, 2024 by RoriCremer Loading…
DRAFT: Use temp snapshot of htsjdk with rans refactoring.
#8730 opened Mar 11, 2024 by cmnbroad • Draft
Test out the preview version of the next GKL (DO NOT MERGE)
#8712 opened Mar 4, 2024 by droazen Loading…
@jamesemery
15
Vs 299 spike speed up integration tests
#8706 opened Feb 29, 2024 by koncheto-broad • Draft
Remove hdfs support for GenomicsDB
#8698 opened Feb 16, 2024 by nalinigans • Draft
Refactoring a confusing method in GATKVariantContextUtils
#8690 opened Feb 13, 2024 by lbergelson • Draft
6
Combining aws-java-nio-spi-for-s3 with GATK.
#8672 opened Feb 1, 2024 by DanishIntizar Loading…
2
Adds option to write sample names in variantCounts
#8656 opened Jan 15, 2024 by odcambc • Draft
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