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Pull requests: broadinstitute/gatk

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Pull requests list

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 Loading…
70
Complex SV intervals support
#8521 opened Sep 15, 2023 by mwalker174 Loading…
15
Gg vs 887 streamline vat tsv extract
#8508 opened Aug 30, 2023 by gbggrant • Draft
10
Install the python-is-python3 package in our docker build
#8499 opened Aug 25, 2023 by droazen Loading…
1
@lbergelson
3
Update to gatk script to contain custom jdk path parameter
#8495 opened Aug 25, 2023 by gokalpcelik Loading…
8
Added percentage complete and expected time remaining to ProgressMeter
#8486 opened Aug 18, 2023 by jonn-smith Loading…
@droazen
5
The VariantFiltration docs said that you can specify that it should remove the filtered variants, which does not seem to be accurate
#8410 opened Jul 11, 2023 by KevinCLydon Loading…
setup_gcnvkernel.py: Add missing pyvcf dependency
#8341 opened May 24, 2023 by jmarshall Loading…
DRAFT: Changes for htsjdk VCFHeader refactoring
#8306 opened May 2, 2023 by cmnbroad • Draft
12
fix insufficient MaxProbPropagationDistance
#8294 opened Apr 24, 2023 by TomofumiSaka Loading…
fix wrong spanning deletion length with NON_REF of HaplotypeCaller
#8292 opened Apr 19, 2023 by TomofumiSaka Loading…
Experimental patch to ReferenceConfidenceVariantContextMerger for the GVS team
#8288 opened Apr 13, 2023 by droazen Loading…
4
fix for https://github.com/broadinstitute/gatk/issues/7304 ( haploid genotype and mendelian violations )
#8279 opened Apr 6, 2023 by lindenb Loading…
1
Added the option to supply multiple mask files to VariantFiltration
#8237 opened Mar 9, 2023 by KevinCLydon • Draft
Add a --numeric-gt option to VariantsToTable
#8219 opened Feb 22, 2023 by lbergelson Loading…
1
2
Add GCC OpenMP library to list of GATK requirements in the README
#8196 opened Feb 10, 2023 by droazen Loading…
1
@lbergelson
6
Vs 778 spike import limit
#8190 opened Feb 6, 2023 by koncheto-broad • Draft
1
Addresses issue #7185
#8189 opened Feb 6, 2023 by vruano Loading…
1
Ah rate limit ingestion
#8188 opened Feb 6, 2023 by koncheto-broad • Draft
1
**DO NOT MERGE** Added features for CompareReferences tool
#8163 opened Jan 18, 2023 by orlicohen Loading…
@droazen
2
ProTip! Find all pull requests that aren't related to any open issues with -linked:issue.