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Pull requests: broadinstitute/gatk

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Pull requests list

VS-1395 Have create vat from vds optionally take sites only vcf
#8851 opened May 28, 2024 by gbggrant • Draft
bq query audit [VS-1396]
#8847 opened May 23, 2024 by mcovarr Loading…
11
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
Fixed a bug in AlleleFiltering that ignored more than a single sample
#8841 opened May 18, 2024 by ilyasoifer Loading…
Mutect2 germline resource can have split multiallelic format
#8837 opened May 16, 2024 by davidbenjamin Loading…
@jamesemery
5
Update the large CRAM files to v3.0.
#8832 opened May 14, 2024 by cmnbroad Loading…
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
9
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
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