Commits · 0c858996c51304613ccd842e6368f256de2a3816 · Mirrors / biopet.biopet

Aug 26, 2014
- Replace SortSam to AddOrReplaceReadGroups for Bowtie · 0c858996
  Peter van 't Hof authored 10 years ago
  
  0c858996
- Changed default aligner to bowtie · 337ef542
  Peter van 't Hof authored 10 years ago
  
  337ef542
- Moved aligners to functions and added Bowtie · 34f65445
  Peter van 't Hof authored 10 years ago
  
  34f65445
- Added defaultAligner var · 81fd15f8
  Peter van 't Hof authored 10 years ago
  
  81fd15f8
- Added skipMarkduplicates on dedup step · 7b626832
  Peter van 't Hof authored 10 years ago
  
  7b626832
- Fix on option on picard · c8ffb442
  Peter van 't Hof authored 10 years ago
  
  c8ffb442
- Fix on final jobs · bbe9311d
  Peter van 't Hof authored 10 years ago
  
  bbe9311d
- Fix deps for prefix Job · cd66d051
  Peter van 't Hof authored 10 years ago
  
  cd66d051
- Fix bug on spaced files name · d1991c9e
  Peter van 't Hof authored 10 years ago
  
  d1991c9e
- Merge commit '80ba94d1 ' into peter · 564dfea2
  Peter van 't Hof authored 10 years ago
  
  564dfea2
- Fix error in biopet-framework pom.xml file · 80ba94d1
  bow authored 10 years ago
  
  80ba94d1
- Fix bug on args · 153c0af2
  Peter van 't Hof authored 10 years ago
  
  153c0af2
Aug 25, 2014
- Added Sage pipeline · 1ddd45ad
  Peter van 't Hof authored 10 years ago
  
  1ddd45ad
- Added -s and -S option · 6b69a6d5
  Peter van 't Hof authored 10 years ago
  
  6b69a6d5
- Fix on args order · 1f6b6d87
  Peter van 't Hof authored 10 years ago
  
  1f6b6d87
- Moved scripts to general package · 3c616b75
  Peter van 't Hof authored 10 years ago
  
  3c616b75
- Merge peter · f3276d72
  Peter van 't Hof authored 10 years ago
  
  f3276d72
- Merge commit 'cfae9015 ' · 4557807c
  Peter van 't Hof authored 10 years ago
  
  Conflicts: flexiprep/nbactions.xml gatk/gatk-pipeline/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkPipeline.scala gatk/gatk-variantcalling/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkVariantcalling.scala mapping/examples/test.json mapping/nbactions.xml pom.xml
  4557807c
- OutputName change · cfae9015
  Peter van 't Hof authored 10 years ago
  
  cfae9015
- Merge all maven packages into 1 · 7624b929
  Peter van 't Hof authored 10 years ago
  
  7624b929
- Added BiopetPackage as complete package · 4f6ea975
  Peter van 't Hof authored 10 years ago
  
  4f6ea975
- Added single sample UnifiedGenotyper · 33b1e8fc
  Peter van 't Hof authored 10 years ago
  
  33b1e8fc
Aug 22, 2014
- Remove old functions · 4f24e9f3
  Peter van 't Hof authored 10 years ago
  
  4f24e9f3
- convert AddOrReplaceReadGroups to biopet function · 3decab94
  Peter van 't Hof authored 10 years ago
  
  3decab94
- convert MergeSamFiles to biopet function · dfed2154
  Peter van 't Hof authored 10 years ago
  
  dfed2154
- Added skipMetrics option · 9b20e271
  Peter van 't Hof authored 10 years ago
  
  9b20e271
- Added allSitePLs option · f6bbd1b0
  Peter van 't Hof authored 10 years ago
  
  f6bbd1b0
- Convert SortSam to biopet function · f66115cc
  Peter van 't Hof authored 10 years ago
  
  f66115cc
Aug 20, 2014
- Merge origin/sander into peter · 2cd4fb00
  Peter van 't Hof authored 10 years ago
  
  2cd4fb00
- Added BamOutput Option to Haplotypecaller · 8e97fe15
  Peter van 't Hof authored 10 years ago
  
  8e97fe15
- Merge commit 'feeafebb ' into sander · 38acf7e0
  sajvanderzeeuw authored 10 years ago
  
  38acf7e0
- Fix bug on single end library's · feeafebb
  Peter van 't Hof authored 10 years ago
  
  feeafebb
- changed mem limit to 4gb · b68ea4a6
  sajvanderzeeuw authored 10 years ago
  
  b68ea4a6
- Merge commit '18e080e1 ' into sander · 20871e07
  sajvanderzeeuw authored 10 years ago
  
  20871e07
Aug 19, 2014
- added all BWA options · d0768d9f
  sajvanderzeeuw authored 10 years ago
  
  d0768d9f
- Moved Flexiprep val to root op mapping class · 18e080e1
  Peter van 't Hof authored 10 years ago
  
  18e080e1
- Remove version command for picard · 89121481
  Peter van 't Hof authored 10 years ago
  
  89121481
- Debug sickle wrapper · 7ab284fd
  sajvanderzeeuw authored 10 years ago
  
  7ab284fd
- Fix bug when json parse failed · 3946dd26
  Peter van 't Hof authored 10 years ago
  
  3946dd26
Aug 18, 2014
- Fix bug on single end bam files · 22fdb87e
  Peter van 't Hof authored 10 years ago
  
  22fdb87e