Commits · 3b0a72426bf6d5b51e9dbf20a5651c8642f29ac5 · Mirrors / biopet.biopet

Jul 18, 2014
- update for Queue/GATK 3.2-2 · 3b0a7242
  Peter van 't Hof authored 10 years ago
  
  3b0a7242
Jul 15, 2014
- Update to Queue/GATK 3.2 · 0a33b3d3
  Peter van 't Hof authored 10 years ago
  
  0a33b3d3
- Code style fix · d6a28af2
  Peter van 't Hof authored 10 years ago
  
  d6a28af2
Jul 03, 2014
- Indel realign is now intermediate · bb32c1aa
  Peter van 't Hof authored 10 years ago
  
  bb32c1aa
- Test file changes · b42ce554
  Peter van 't Hof authored 10 years ago
  
  b42ce554
- Added dependency for bam-metrics · 97cf8080
  Peter van 't Hof authored 10 years ago
  
  97cf8080
- Switched to biopet markduplicates · 9add492d
  Peter van 't Hof authored 10 years ago
  
  9add492d
Jun 26, 2014
- Added config report · 71a74799
  Peter van 't Hof authored 10 years ago
  
  71a74799
- Added stand_call_conf and stand_emit_conf as config option · 40c694ad
  Peter van 't Hof authored 10 years ago
  
  40c694ad
Jun 23, 2014
- pom changes for start of 0.1.3 · 9e9e6022
  Peter van 't Hof authored 10 years ago
  
  9e9e6022
- Thread options does not work anymore from QScript · b9325173
  Peter van 't Hof authored 10 years ago
  
  b9325173
- Changed constructors · ea4f80e1
  Peter van 't Hof authored 10 years ago
  
  ea4f80e1
Jun 21, 2014
- Config changed · c22acb87
  Peter van 't Hof authored 10 years ago
  
  c22acb87
Jun 19, 2014
- Readme changed to README.md · a33d9fd2
  Peter van 't Hof authored 10 years ago
  
  a33d9fd2
- Path to class for main class changed · 90e96f6c
  Peter van 't Hof authored 10 years ago
  
  90e96f6c
- Packaging changed, no scala compiler anymore in jar · 27de6356
  Peter van 't Hof authored 10 years ago
  
  27de6356
Jun 17, 2014
- version changes · f0705ac8
  Peter van 't Hof authored 10 years ago
  
  removing source files from jar packaging
  f0705ac8
Jun 13, 2014
- Rename directories and package identifiers for consistency with Queue · 4e14ca72
  bow authored 10 years ago
  
  4e14ca72
Jun 12, 2014
- Skipped compiling step at init phase of pipeline · e031256a
  Peter van 't Hof authored 10 years ago
  
  e031256a
Jun 10, 2014
- example jsons changed/added · 5b01a7d9
  Peter van 't Hof authored 10 years ago
  
  5b01a7d9
- SplitNCigarReads now before indel realign · 35f10a6b
  Peter van 't Hof authored 10 years ago
  
  35f10a6b
Jun 09, 2014
- Added rna mode for inputtype · d46c0d7d
  Peter van 't Hof authored 10 years ago
  
  d46c0d7d
- getThreads function implemented in gatk functions · 7e7762a9
  Peter van 't Hof authored 10 years ago
  
  7e7762a9
Jun 03, 2014
- Added VariantAnnotator step · 31460c83
  Peter van 't Hof authored 10 years ago
  
  31460c83
- Added single QScript for for VariantAnnotator, not used in Gatk pipeline · 73053fa3
  Peter van 't Hof authored 10 years ago
  
  73053fa3
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
- Gatk now uses the mapping module · b3553528
  Peter van 't Hof authored 10 years ago
  
  b3553528
- Added scala files to jar and added a main class for each pipeline · 302c6fff
  Peter van 't Hof authored 10 years ago
  
  302c6fff
May 21, 2014
- - Added sub configs for gatk buildin modules · f95148c6
  Peter van 't Hof authored 10 years ago
  
  f95148c6
- - 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 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