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Pull requests: broadinstitute/gatk

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Pull requests list

Half-bad hetvars, VCF edition: one bad allele fails the genotype [VS-1615]
#9149 opened Apr 14, 2025 by mcovarr • Draft
Drop samples from VDS during merge and rescore [VS-1641]
#9147 opened Apr 14, 2025 by mcovarr Loading…
Potential fix for code scanning alert no. 15: Implicit narrowing conversion in compound assignment
#9146 opened Apr 13, 2025 by lbergelson Loading…
1
VS-1178 merge master into ah var store again
#9135 opened Apr 1, 2025 by gbggrant • Draft
10
Add the Clinvar Review Status as a filter
#9134 opened Mar 31, 2025 by RoriCremer Loading…
9
Update hadoop 3.3.6 -> 3.4.0
#9132 opened Mar 28, 2025 by lbergelson Loading…
2
Add variant stratification and overlap metrics in SVConcordance
#9125 opened Mar 24, 2025 by mwalker174 Loading…
16
Intel GKL-PDHMM update
#9123 opened Mar 24, 2025 by chirayuharyan Loading…
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
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…
9
[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
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
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