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Pull requests: broadinstitute/gatk
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Updated Python and PyMC, removed TensorFlow, and added PyTorch in conda environment.
#8561
opened Oct 23, 2023 by
samuelklee
•
Draft
Removed restriction that physical phasing may only be run in ERC modes.
#5772
opened Mar 7, 2019 by
tfenne
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Added in code to populate the name of VariantContext objects.
Engine
#4571
opened Mar 23, 2018 by
jonn-smith
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(Do not merge) Port of nvscorevariants into GATK, with a basic tool frontend
#8004
opened Aug 26, 2022 by
droazen
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Adding in default value for funcotator transcript selection list.
#5872
opened Apr 9, 2019 by
jonn-smith
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Subsetting for A-length annotations (e.g. AF, PRI, F1R2, F2R1),
#7725
opened Mar 15, 2022 by
ldgauthier
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genotypingEngine seems to have a bug in the logic in the presence of ambiguous alleles.
#6363
opened Jan 9, 2020 by
yfarjoun
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Added a useful debugging output mode that prints a summary of every assembly region
assembly
enhancement
#6441
opened Feb 4, 2020 by
jamesemery
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Adding new argument to control variant output interval filtering.
#6388
opened Jan 17, 2020 by
lbergelson
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Changed ReferenceConfidenceModel to use offsetlength counting deletions for ending comparisons
bug
JointCalling
#5665
opened Feb 12, 2019 by
jamesemery
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Memory-less HMM transition matrix for baseline copy-number states and silent CNV classes
Copy Number tools
Germline CNV
#4988
opened Jul 6, 2018 by
mbabadi
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Changed exact-match tests for ModelSegments to allow for numerical differences due to Java version.
#8111
opened Nov 29, 2022 by
samuelklee
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(DO NOT MERGE) Draft PR for reimplementation of annotation-based filtering tools.
#7659
opened Jan 31, 2022 by
samuelklee
•
Draft
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