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NationalGenomicsInfrastructure
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piper
A genomics pipeline build on top of the GATK Queue framework
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specify target jvm
#88
b97pla
closed
7 years ago
0
run clean as TwoCoreJob to allow more RAM, only separate indels and s…
#87
b97pla
closed
7 years ago
2
Fixed typos and added extra information regarding Picard
#86
monikaBrandt
closed
7 years ago
0
Standalone genotype concordance workflow
#85
b97pla
closed
7 years ago
1
Explicitly pass bam file to genotype
#84
b97pla
closed
7 years ago
1
Fix missing variant eval and eval raw variants
#83
johandahlberg
closed
7 years ago
0
FixEmptyReads.pl not bundled in Piper 1.4.0
#82
johanherman
closed
5 years ago
0
Devel
#81
b97pla
closed
8 years ago
2
Feature/multiple version support
#80
johandahlberg
closed
8 years ago
3
Use qualimap with flag skip duplicated
#79
Smeds
closed
8 years ago
1
Feature/disable phone home
#78
b97pla
closed
8 years ago
1
New qualimap version and option
#77
Smeds
closed
8 years ago
6
Devel
#76
b97pla
closed
8 years ago
0
bump version
#75
b97pla
closed
8 years ago
1
Devel
#74
b97pla
closed
8 years ago
1
Feature/reduce delivery footprint
#73
b97pla
closed
8 years ago
2
Fixed typo in version report
#72
PerLundmark
closed
8 years ago
1
Fixed typo in version report
#71
PerLundmark
closed
8 years ago
2
Feature/reduce delivery footprint
#70
b97pla
closed
8 years ago
1
properly skip recalibration
#69
b97pla
closed
8 years ago
1
implement compressing vcfs by gatk, and flag to disable
#68
b97pla
closed
8 years ago
3
calculate checksums for the produced files
#67
b97pla
closed
8 years ago
1
Support compressing vcf files
#66
b97pla
closed
8 years ago
0
add logo + resources
#65
robinandeer
closed
9 years ago
4
Ordering error in setup file creation
#64
johandahlberg
opened
9 years ago
0
Not enough memory, better way to determine Xmx value
#63
biocyberman
opened
9 years ago
5
Spelling error: sequenceingcenter -> sequencingcenter
#62
johandahlberg
closed
9 years ago
0
Generate snpEff html
#61
parlundin
opened
9 years ago
0
SnpEff ends up in wrong place in dependency graph for exome runs
#60
johandahlberg
opened
9 years ago
0
Question: is it intentional to leave out minimumBaseQuality from HaplotypeCallerBase?
#59
biocyberman
closed
9 years ago
1
Maybe a bug: Qualimap step does not detect failure
#58
biocyberman
opened
9 years ago
1
Incorrect paths for index and reference files when running RNAcounts workflow
#57
jessieno
opened
9 years ago
0
Question: How to rerun from a particular analysis step?
#56
biocyberman
closed
9 years ago
2
Error in README
#55
jessieno
closed
9 years ago
0
Piper failed for a sample with a name that looks like '3-NOP'
#54
jessieno
closed
9 years ago
0
Update bwa
#53
johandahlberg
closed
9 years ago
0
To allow institution-specific setup
#52
biocyberman
closed
7 years ago
9
To allow institution-specific setup
#51
biocyberman
closed
9 years ago
0
Bug: Can't detect 'path' not set for a resource or program
#50
biocyberman
closed
9 years ago
2
Coverage not correct
#49
parlundin
opened
9 years ago
3
Less memory for samtools sort
#48
johandahlberg
closed
9 years ago
3
Update VQSR parameters
#47
johandahlberg
closed
9 years ago
0
Update to GATK 3.3
#46
johandahlberg
closed
9 years ago
0
Some questions before adoption of piper
#45
biocyberman
opened
9 years ago
3
Upgrade to Qualimap 2.0
#44
parlundin
closed
9 years ago
4
Add snpEff
#43
ewels
closed
9 years ago
22
Question for the man
#42
mariogiov
closed
9 years ago
2
Picard metrics file deleted
#41
ewels
closed
9 years ago
4
Just one sample in delivery folder when running multiple samples
#40
parlundin
opened
9 years ago
3
Genotype concordance error
#39
mariogiov
closed
9 years ago
1
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