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Pull requests: broadinstitute/gatk

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Pull requests list

VS 1528 Update the sharding of the samples in the VAT creation to be dependent on the number of samples
#9039 opened Nov 13, 2024 by RoriCremer Loading…
VS-1526 - Fix error in Extract Manifest Creation causing it to run forever.
#9034 opened Nov 5, 2024 by gbggrant Loading…
2
Maximum alt alleles guardrail [VS-1530]
#9033 opened Nov 5, 2024 by mcovarr Loading…
5
Retain all source IDs on VariantContext merge + test
#9032 opened Nov 4, 2024 by bbimber Loading…
1
Yyu test 1
#9026 opened Oct 30, 2024 by yonghaoy • Draft
optional column call_ps
#9025 opened Oct 30, 2024 by yonghaoy Loading…
1
BQSR: avoid throwing an error when read group is missing in the recal table, and some refactoring.
#9020 opened Oct 28, 2024 by takutosato Loading…
@davidbenjamin
VS-1490 - Refactor python code from extract dir into a scripts directory.
#9017 opened Oct 23, 2024 by gbggrant Loading…
4
Create tools for SV VCF cleaning
#8996 opened Oct 9, 2024 by kjaisingh • Draft
@kjaisingh
22
Add SVStratify and GroupedSVCluster tools
#8990 opened Oct 2, 2024 by mwalker174 Loading…
66
FlowFeatureMapper speed improvements
#8982 opened Sep 16, 2024 by dror27 • Draft
12
Add a few additional failures to our notes doc
#8980 opened Sep 15, 2024 by RoriCremer Loading…
26
Bundle support for FeatureInputs, references; add CreateBundle tool.
#8944 opened Aug 6, 2024 by cmnbroad • Draft
[DRAFT] Merge master to ah var store again [VS-1178]
#8890 opened Jun 24, 2024 by mcovarr • Draft
1
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
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
vs 1372 excess alt alleles -- set limit to 3 for a test
#8843 opened May 22, 2024 by RoriCremer • Draft
1
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…
1
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…
18
DRAFT: Use temp snapshot of htsjdk with rans refactoring.
#8730 opened Mar 11, 2024 by cmnbroad • Draft
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