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Use sequence dictionaries from interval files, when present
Engine
#301
opened Mar 12, 2015 by
droazen
Refactor GATKVariantContextUtils' variant context merging methods.
coding
#132
opened Jan 20, 2015 by
vruano
Use StandardArgumentDefinitions for arguments
CLI
Documentation
Help Wanted (Community)
PRIORITY_LOW
QuixoticDream
#133
opened Jan 21, 2015 by
lbergelson
Make it possible to define min/max and disabling values for numeric argument values
CLI
Documentation
enhancement
PRIORITY_LOW
#143
opened Jan 22, 2015 by
vdauwera
Unify classes that represent Genomic intervals
coding
QuixoticDream
#159
opened Jan 26, 2015 by
lbergelson
Integration tests: add a way for intelligent comparison of files of different formats
enhancement
tests
#190
opened Feb 19, 2015 by
akiezun
Add a javadoc checking step to the build
Documentation
enhancement
PRIORITY_LOW
ReleaseEngineering
#261
opened Mar 7, 2015 by
akiezun
Ported from Classic-GATK: Resolve forked dangling ends in assembly graph
enhancement
HaplotypeCaller
#266
opened Mar 7, 2015 by
vdauwera
Delete R code (and move the functionality elsewhere)
Help Wanted (Community)
QuixoticDream
#292
opened Mar 12, 2015 by
akiezun
Allow intervals to be parsed in IntervalArgumentCollection without a sequence dictionary
Engine
#298
opened Mar 12, 2015 by
droazen
Make all input arguments auto-discoverable and mark as @AutoDiscoverable
CLI
Engine
enhancement
QuixoticDream
#300
opened Mar 12, 2015 by
droazen
Add a check in FeatureDataSource that intervals are sorted/merged properly
Engine
#327
opened Mar 23, 2015 by
droazen
Document that ReadWalkers can receive unmapped reads when there is an interval list.
#430
opened Apr 22, 2015 by
vruano
Standardize test data location and naming
coding
QuixoticDream
tests
#445
opened Apr 24, 2015 by
lbergelson
Validate all existing test BAMs
Help Wanted (Community)
QuixoticDream
tests
#569
opened Jun 16, 2015 by
lbergelson
Unify read comparators in hellbender
Engine
PRIORITY_LOW
QuixoticDream
#620
opened Jul 8, 2015 by
droazen
Determine how to manage test data in the gs://hellbender bucket
Spark
tests
#739
opened Jul 23, 2015 by
droazen
GATK4.5.0.0 HaplotypeCaller exits with error code 245 while no error message
#9104
opened Feb 28, 2025 by
Alipha-Clisa
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