Commits · 31460c830a67ff1f99f74f811918b5592a6a8ae4 · Mirrors / biopet.biopet · GitLab

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Jun 03, 2014
- Added VariantAnnotator step · 31460c83
  Peter van 't Hof authored 10 years ago
  
  31460c83
- Added shading for framework, Queue is now included in the jar of the framework · d5a50842
  Peter van 't Hof authored 10 years ago
  
  d5a50842
- Changed filenames for compatible summarize script · 171522f4
  Peter van 't Hof authored 10 years ago
  
  171522f4
- Added single QScript for for VariantAnnotator, not used in Gatk pipeline · 73053fa3
  Peter van 't Hof authored 10 years ago
  
  73053fa3
- BiopetQScript is now abstract · 80512eba
  Peter van 't Hof authored 10 years ago
  
  80512eba
- Changed to make it compatible for new file structure · 97fd01f3
  Peter van 't Hof authored 10 years ago
  
  97fd01f3
- Added Summarize flexiprep wrapper · f9d9430b
  Peter van 't Hof authored 10 years ago
  
  f9d9430b
- Added Seqstat wrapper · a98ad7f7
  Peter van 't Hof authored 10 years ago
  
  a98ad7f7
- Added Sha1sum wrapper · 157d6e8d
  Peter van 't Hof authored 10 years ago
  
  157d6e8d
- Added Ln wrapper · 59459ae6
  Peter van 't Hof authored 10 years ago
  
  59459ae6
May 27, 2014
- Added general trait (BiopetQScript) that now have multisample functions · 09190f82
  Peter van 't Hof authored 10 years ago
  
  09190f82
May 26, 2014
- Moved aligners to own package · 5d0b4fc9
  Peter van 't Hof authored 10 years ago
  
  5d0b4fc9
- Gatk now uses the mapping module · b3553528
  Peter van 't Hof authored 10 years ago
  
  b3553528
- Small changes on config setup · 8d195010
  Peter van 't Hof authored 10 years ago
  
  8d195010
- Added default_clip_mode option · b0317762
  Peter van 't Hof authored 10 years ago
  
  b0317762
- Added scala files to jar and added a main class for each pipeline · 302c6fff
  Peter van 't Hof authored 10 years ago
  
  302c6fff
- Added python parser to buildin python scripts · 2f38f1f1
  Peter van 't Hof authored 10 years ago
  
  2f38f1f1
- Added python scripts to jar file · 9519ee04
  Peter van 't Hof authored 10 years ago
  
  9519ee04
May 21, 2014
- - Standerize config · 2fb73c96
  Peter van 't Hof authored 10 years ago
  
  2fb73c96
- - Fixed output file for star · 30fe43b7
  Peter van 't Hof authored 10 years ago
  
  30fe43b7
- - Fixed output file · bb158f36
  Peter van 't Hof authored 10 years ago
  
  bb158f36
- - Added sub configs for gatk buildin modules · f95148c6
  Peter van 't Hof authored 10 years ago
  
  f95148c6
- - Fixed scattercounts · 31ea0eee
  Peter van 't Hof authored 10 years ago
  
  31ea0eee
- - Fixed scattercounts · 630092d5
  Peter van 't Hof authored 10 years ago
  
  630092d5
- - Fixed scattercounts · 307c0b53
  Peter van 't Hof authored 10 years ago
  
  307c0b53
- - output file for star · da6a6ef2
  Peter van 't Hof authored 10 years ago
  
  da6a6ef2
- - output file for star · 23084ff1
  Peter van 't Hof authored 10 years ago
  
  23084ff1
May 20, 2014
- - fixed thread option for star · de498a26
  Peter van 't Hof authored 10 years ago
  
  de498a26
- - fixed namespaceing in AddOrReplaceReadGroups · da66790f
  Peter van 't Hof authored 10 years ago
  
  da66790f
- - fixed namespaceing in AddOrReplaceReadGroups · eb23b56e
  Peter van 't Hof authored 10 years ago
  
  eb23b56e
- - Fixed output of star · 6ebb058a
  Peter van 't Hof authored 10 years ago
  
  6ebb058a
- - Fixed input field on markduplicates in mapping module · 4785e578
  Peter van 't Hof authored 10 years ago
  
  4785e578
- - Fixed scattercount in Variant Recalibration · 205355eb
  Peter van 't Hof authored 10 years ago
  
  205355eb
- - Fixed memory issue in Variant Recalibration · 3f2913f8
  Peter van 't Hof authored 10 years ago
  
  3f2913f8
- - Fixed Bwa on Gatk, did called the wrong config · 379c8474
  Peter van 't Hof authored 10 years ago
  
  379c8474
- - Added referenceFile to catVariants · b1276a90
  Peter van 't Hof authored 10 years ago
  
  b1276a90
- - Added nt and scattercount options to ApplyRecalibration · 08f3651d
  Peter van 't Hof authored 10 years ago
  
  08f3651d
- - Added wrapper for Star · ca2905e5
  Peter van 't Hof authored 10 years ago
  
  - Added a mapping module (not yet used in Gatk) - Added VariantRecalibrator to Gatk
  ca2905e5
May 15, 2014
- Remove submodules · b26d817a
  Peter van 't Hof authored 10 years ago
  
  b26d817a
- remove submodules · ffe46a1f
  Peter van 't Hof authored 10 years ago
  
  ffe46a1f