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Pull requests: broadinstitute/gatk

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Pull requests list

Update HTSJDK to 4.1.1 and Picard to 3.2.0
#8900 opened Jun 28, 2024 by droazen Loading…
VS-1417 address ad issue in extracted vc fs
#8899 opened Jun 28, 2024 by gbggrant • Draft
Modified HaplotypeBasedVariantRecaller to support non-flow reads
#8896 opened Jun 26, 2024 by ilyasoifer Loading…
FlowFeatureMapper: X_FILTERED_COUNT semantics adjusted and documented more accurately
#8894 opened Jun 26, 2024 by dror27 Loading…
[DRAFT] Merge master to ah var store again [VS-1178]
#8890 opened Jun 24, 2024 by mcovarr • Draft
1
Handle CTX_PP/QQ and CTX_PQ/QP CPX_TYPE values in SVConcordance
#8885 opened Jun 21, 2024 by epiercehoffman Loading…
3
Code Review for #8752
#8871 opened Jun 13, 2024 by bbimber Loading…
4
Extract the revision 1 / "full" filter tables only [VS-1409]
#8868 opened Jun 11, 2024 by mcovarr Loading…
4
Add utilites to update Echo filters and reference genotypes
#8867 opened Jun 11, 2024 by chrisvittal Loading…
6
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
8
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
vs 1372 excess alt alleles -- set limit to 3 for a test
#8843 opened May 22, 2024 by RoriCremer • Draft
1
Update the large CRAM files to v3.0.
#8832 opened May 14, 2024 by cmnbroad Loading…
3
Diagnostics.
#8819 opened May 7, 2024 by cmnbroad Loading…
@droazen
3
Added long read walkers from long-running branch.
#8799 opened Apr 29, 2024 by jonn-smith Loading…
32
⛔ [DO NOT MERGE] ⛔ Fix partition grouping bug ⛔
#8785 opened Apr 21, 2024 by mcovarr Loading…
add echocallset as an option for integration test
#8757 opened Apr 1, 2024 by RoriCremer Loading…
Retain all source IDs on VariantContext merge + test
#8752 opened Mar 26, 2024 by lbergelson Loading…
16
Retain all source IDs on VariantContext merge
#8750 opened Mar 25, 2024 by bbimber Loading…
1
DRAFT: Use temp snapshot of htsjdk with rans refactoring.
#8730 opened Mar 11, 2024 by cmnbroad • Draft
Leave validation cluster running at end [VS-901]
#8729 opened Mar 11, 2024 by mcovarr Loading…
Test out the preview version of the next GKL (DO NOT MERGE)
#8712 opened Mar 4, 2024 by droazen Loading…
@jamesemery
2
Vs 299 spike speed up integration tests
#8706 opened Feb 29, 2024 by koncheto-broad • Draft
ProTip! Exclude everything labeled bug with -label:bug.