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Failure using samtools-generated .idx/.dict when reference has ambiguity code "."
#3306
opened Jul 19, 2017 by
cmnbroad
updated Jul 19, 2017
Need a unified mechanism for referencing the application name in various outputs
#3312
opened Jul 19, 2017 by
cmnbroad
updated Jul 20, 2017
SATagBuilder Api to manage SA:Z:* tags could be improved.
coding
enhancement
#3324
opened Jul 21, 2017 by
vruano
updated Jul 21, 2017
Improve HC Sensitivity with UG
QuixoticDream
#3420
opened Aug 8, 2017 by
skwalker
updated Aug 8, 2017
TableCodec isn't properly indexable due to buffering done by OpenCSV reader.
#3440
opened Aug 14, 2017 by
cmnbroad
updated Aug 14, 2017
fail travis build if before_install / install blocks fail
tests
#3444
opened Aug 14, 2017 by
lbergelson
updated Aug 14, 2017
Improve long read alignment filtering tool
enhancement
SV
#3473
opened Aug 22, 2017 by
SHuang-Broad
updated Aug 22, 2017
Implement pre/post ReadTransformer code in GATKSparkTool
#3484
opened Aug 23, 2017 by
magicDGS
updated Aug 23, 2017
Catching when SAM with .bam extension is loaded in Spark
BWA
hadoop-bam
#3488
opened Aug 23, 2017 by
mwalker174
updated Aug 25, 2017
Want an engine feature to convert XT tagged base qualities to two
#3540
opened Sep 1, 2017 by
sooheelee
updated Sep 1, 2017
BucketUtils does not make use of FileSystemProviders.installedProviders()
Engine
enhancement
question
#3569
opened Sep 12, 2017 by
vruano
updated Sep 12, 2017
Add test for DataProvider failures
tests
#3619
opened Sep 27, 2017 by
lbergelson
updated Sep 27, 2017
Check for google-cloud-sdk compatibility with GATK in launcher
Vanilla
#3649
opened Oct 2, 2017 by
chandrans
updated Oct 2, 2017
manage_sv_pipeline.sh output directory naming issues with a detached checkout
bug
SV
#3642
opened Oct 1, 2017 by
vruano
updated Oct 3, 2017
update the gradle default assembleDist task
BuildSystem
#3059
opened Jun 7, 2017 by
lbergelson
updated Oct 17, 2017
git-lfs problems when updating a fork after the protected merge
bug
tests
#3038
opened Jun 6, 2017 by
lbergelson
updated Oct 17, 2017
Allow intervals to be parsed in IntervalArgumentCollection without a sequence dictionary
Engine
#298
opened Mar 12, 2015 by
droazen
updated Oct 17, 2017
Determine how to manage test data in the gs://hellbender bucket
Spark
tests
#739
opened Jul 23, 2015 by
droazen
updated Oct 17, 2017
spark tools on local give no progress for a long time
Spark
#1294
opened Dec 9, 2015 by
akiezun
updated Oct 17, 2017
Improve error message in spark tools when trying to access a local file from other nodes
bug
hadoop-bam
Spark
#1417
opened Jan 6, 2016 by
akiezun
updated Oct 17, 2017
Implement CRAMReferenceSource for 2bit references
#1443
opened Jan 22, 2016 by
cmnbroad
updated Oct 17, 2017
Add output indexing on the fly for Spark tools
#1480
opened Feb 11, 2016 by
cmnbroad
updated Oct 17, 2017
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Updated in the last three days: updated:>2024-07-02.