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Issues list

Refactor GATKVariantContextUtils' variant context merging methods. coding
#132 opened Jan 20, 2015 by vruano updated Jan 20, 2015
1
Tracker for unmodifiableMap Kryo workaround Spark
#874 opened Sep 2, 2015 by davidadamsphd updated Sep 7, 2015
Consider running Travis Spark tests against EMR Spark Help Wanted (Community) Spark
#885 opened Sep 9, 2015 by laserson updated Oct 5, 2015
CollectWGSMetrics in Spark Metrics Picard Spark
#1039 opened Oct 22, 2015 by akiezun updated Oct 28, 2015
Need CRAM equivalent of BAM block copying operation
#1163 opened Nov 19, 2015 by cmnbroad updated Nov 19, 2015
RevertBaseQualityScoresIntegrationTest needs CRAM tests Picard tests
#1232 opened Dec 2, 2015 by akiezun updated Dec 2, 2015
Add tests for different dup scoring strategies to AbstractMarkDuplicatesCommandLineProgramTest tests
#1245 opened Dec 3, 2015 by akiezun updated Dec 3, 2015
Unify classes that represent Genomic intervals coding QuixoticDream
#159 opened Jan 26, 2015 by lbergelson updated Jan 5, 2016
1
Delete R code (and move the functionality elsewhere) Help Wanted (Community) QuixoticDream
#292 opened Mar 12, 2015 by akiezun updated Jan 5, 2016
2
Make all input arguments auto-discoverable and mark as @AutoDiscoverable CLI Engine enhancement QuixoticDream
#300 opened Mar 12, 2015 by droazen updated Jan 5, 2016
5
Validate all existing test BAMs Help Wanted (Community) QuixoticDream tests
#569 opened Jun 16, 2015 by lbergelson updated Jan 5, 2016
12
Unify read comparators in hellbender Engine PRIORITY_LOW QuixoticDream
#620 opened Jul 8, 2015 by droazen updated Jan 5, 2016
port "Allow VariantsToTable to determine each allele's type when -SMA is used "
#1428 opened Jan 12, 2016 by akiezun updated Jan 12, 2016
create gradle plugin that automatically configures sparkJar correctly QuixoticDream ReleaseEngineering
#1453 opened Jan 27, 2016 by lbergelson updated Jan 27, 2016
Update serializable objects to use lambda functions where appropriate after upgrading to Kryo 3.0+
#1510 opened Feb 19, 2016 by cwhelan updated Feb 19, 2016
Generalize --forceValidOutput to apply to all tools that write VCFs enhancement
#1483 opened Feb 12, 2016 by vdauwera updated Feb 29, 2016
1
Create unified IndexInput tool
#1545 opened Mar 3, 2016 by lbergelson updated Mar 3, 2016
Investigate whether our default validation stringency for reads should be STRICT rather than SILENT Engine question
#1457 opened Jan 28, 2016 by droazen updated Mar 28, 2016
SortVcf can't read v3.3 vcf file but CountVariants and SelectVariants can
#1304 opened Dec 9, 2015 by cmnbroad updated Mar 28, 2016
3
fix and reenable BaseRecalibratorSparkOptimizedIntegrationTest Spark tests
#1119 opened Nov 13, 2015 by akiezun updated Mar 28, 2016
2
SparkContextFactory should not take a master parameter Spark
#1070 opened Oct 29, 2015 by laserson updated Mar 28, 2016
2
plotting of spark UI metrics to help understand performance enhancement performance Spark
#1658 opened Mar 28, 2016 by akiezun updated Mar 29, 2016
2
VariantFiltration - add a way to filter by AlleleBalance computed on the fly enhancement
#1726 opened Apr 18, 2016 by akiezun updated Apr 18, 2016
Make gathered BQSR tables identical to running without scatter gather enhancement
#1548 opened Mar 3, 2016 by lbergelson updated Apr 19, 2016
2
GenotypeAnnotations require GT, but some fields could be computed without that information community-request
#1730 opened Apr 19, 2016 by magicDGS updated Apr 20, 2016
ProTip! What’s not been updated in a month: updated:<2024-06-03.