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simplify tests that use ReadsProcessingPipelineTestData
coding
tests
#4318
opened Jan 31, 2018 by
lbergelson
updated Jan 31, 2018
figure out what to make of incomplete or ambiguous assembly contigs
enhancement
SV
#4229
opened Jan 22, 2018 by
SHuang-Broad
updated Jan 31, 2018
create a homebrew formula for GATK
Help Wanted (Community)
#4164
opened Jan 16, 2018 by
lbergelson
updated Feb 5, 2018
Spark tools have problems with umlauts
bug
Spark
#4337
opened Feb 5, 2018 by
stefandiederich
updated Feb 6, 2018
Add coverage-based filtering for large deletions
SV
#4372
opened Feb 8, 2018 by
cwhelan
updated Feb 8, 2018
CalculateGenotypePosteriors allows input VCFs from different references
#4383
opened Feb 9, 2018 by
ldgauthier
updated Feb 9, 2018
HaplotypeCaller -contamination argument does not affect AD, but perhaps should
HaplotypeCaller
question
#4412
opened Feb 14, 2018 by
droazen
updated Feb 26, 2018
conda issue? /bin/env python - too many levels of symbolic links
#4459
opened Feb 26, 2018 by
marchoeppner
updated Feb 26, 2018
Recognize structured comment for locatable columns in xsv locatable files
enhancement
#4489
opened Mar 5, 2018 by
LeeTL1220
updated Mar 5, 2018
Reference requirements for intervals could be more clear
#4507
opened Mar 7, 2018 by
ldgauthier
updated Mar 7, 2018
Unpredicted execution time on 32 cores VM
profiling
Spark
#4516
opened Mar 9, 2018 by
Vzzarr
updated Mar 9, 2018
Generate different artifacts/modules for different project components
#3900
opened Dec 1, 2017 by
magicDGS
updated Mar 26, 2018
AnnotatedIntervalCodec has not been tested with NIO
tests
#4579
opened Mar 26, 2018 by
LeeTL1220
updated Mar 26, 2018
TableCodec doesn't handle hg38 intervals correctly
#4597
opened Mar 27, 2018 by
cmnbroad
updated Mar 28, 2018
Allow VariantFiltration "unfilter" variants
Vanilla
#4628
opened Apr 6, 2018 by
chandrans
updated Apr 6, 2018
Added support for inputs from AWS S3 using EMRFS
#2696
opened May 10, 2017 by
mschroering
updated Apr 10, 2018
Spark and mapr
community-request
Help Wanted (Community)
Spark
#3936
opened Dec 7, 2017 by
AxVE
updated Apr 10, 2018
VariantAnnotatorEngine improvements/optimizations
#4658
opened Apr 13, 2018 by
cmnbroad
updated Apr 13, 2018
GATKTool inconsistencies for implementations
#4651
opened Apr 12, 2018 by
magicDGS
updated Apr 13, 2018
2 tasks
Main.getClassList does not allow to include single picard tools
#4660
opened Apr 16, 2018 by
magicDGS
updated Apr 25, 2018
GATKTool could output additional information during stack unwind
question
#4748
opened May 8, 2018 by
lbergelson
updated May 8, 2018
Matplotlib throws RuntimeError when Python is not installed as a framework
Python
#4743
opened May 7, 2018 by
mwalker174
updated May 9, 2018
Funcotator should determine reference version based on the actual given reference sequence
Funcotator
#4772
opened May 15, 2018 by
jonn-smith
updated May 15, 2018
Can we simplify updates to the GENCODE version?
Funcotator
question
#4786
opened May 18, 2018 by
LeeTL1220
updated May 18, 2018
ProTip!
Exclude everything labeled
bug with -label:bug.