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Pull requests: broadinstitute/gatk

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Pull requests list

Mutect2 germline resource can have split multiallelic format
#8837 opened May 16, 2024 by davidbenjamin Loading…
@jamesemery
3
Update the large CRAM files to v3.0.
#8832 opened May 14, 2024 by cmnbroad • Draft
2
Diagnostics.
#8819 opened May 7, 2024 by cmnbroad • Draft
@droazen
3
[BIOIN-1570] Fixed edge case in variant annotation
#8810 opened May 3, 2024 by ilyasoifer Loading…
1
@droazen
2
Added long read walkers from long-running branch.
#8799 opened Apr 29, 2024 by jonn-smith Loading…
1
⛔ [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
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
Reverting the CombineGVCFs and GenotypeGVCFs to the old behavior for no-calls when there are no PLs present.
#8689 opened Feb 13, 2024 by jamesemery Loading…
2
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
LearnReadOrientationModel loads tables for one ref context at a time, reducing memory demands 32x
#8639 opened Jan 4, 2024 by davidbenjamin Loading…
1
1
2023-12-15 master to ah_var_store [DRAFT] [VS-1178]
#8630 opened Dec 15, 2023 by mcovarr • Draft
DRAGEN Joint Detection DO NOT MERGE
#8616 opened Dec 11, 2023 by davidbenjamin Loading…
2
test java 21
#8589 opened Nov 17, 2023 by lbergelson • Draft
1
Updated Python and PyMC, removed TensorFlow, and added PyTorch in conda environment.
#8561 opened Oct 23, 2023 by samuelklee • Draft
44
Complex SV intervals support
#8521 opened Sep 15, 2023 by mwalker174 Loading…
Gg vs 887 streamline vat tsv extract
#8508 opened Aug 30, 2023 by gbggrant • Draft
10
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