Commits · 6294de9f58989903d00ce35de9bc1eff31aecfe5 · Mirrors / biopet.biopet

22 Jul, 2014 1 commit
- Changes in config class · 6294de9f
  Peter van 't Hof authored Jul 22, 2014
  
  6294de9f
21 Jul, 2014 8 commits
- Changed path to Biopet · 385bfef9
  Peter van 't Hof authored Jul 21, 2014
  
  385bfef9
- Added stand_call_conf and stand_emit_conf option · 7734a3c0
  Peter van 't Hof authored Jul 21, 2014
  
  7734a3c0
- Added stand_call_conf and stand_emit_conf option · 9a25fc2b
  Peter van 't Hof authored Jul 21, 2014
  
  9a25fc2b
- Added Alignment Metrics · 1df0bfa4
  Peter van 't Hof authored Jul 21, 2014
  
  1df0bfa4
- Fixed location of jar file · 89926ccd
  Peter van 't Hof authored Jul 21, 2014
  
  89926ccd
- Spelling error · 95ba716f
  Peter van 't Hof authored Jul 21, 2014
  
  95ba716f
- Collected all gatk pipelines/artifacts into 1 maven project · 2f47af7e
  Peter van 't Hof authored Jul 21, 2014
  
  2f47af7e
- Collected all gatk pipelines/artifacts into 1 maven project · 79435a29
  Peter van 't Hof authored Jul 21, 2014
  
  79435a29
18 Jul, 2014 9 commits
- Fix for outputDir · bffb8a1b
  Peter van 't Hof authored Jul 18, 2014
  
  bffb8a1b
- Fix for Queue-3.2-2 · 94c23ca3
  Peter van 't Hof authored Jul 18, 2014
  
  94c23ca3
- Added 2 modules · 9be6e744
  Peter van 't Hof authored Jul 18, 2014
  
  9be6e744
- Added a benchmark pipeline for gvcf · ea95c71d
  Peter van 't Hof authored Jul 18, 2014
  
  ea95c71d
- Added GatkPipeline, finaly replacement for "Gatk" pipeline · f49e6275
  Peter van 't Hof authored Jul 18, 2014
  
  f49e6275
- Added min_mapping_quality_score to haplotypecaller · ae952d4c
  Peter van 't Hof authored Jul 18, 2014
  
  ae952d4c
- update for Queue/GATK 3.2-2 · 62ed4c90
  Peter van 't Hof authored Jul 18, 2014
  
  62ed4c90
- update for Queue/GATK 3.2-2 · 3b0a7242
  Peter van 't Hof authored Jul 18, 2014
  
  3b0a7242
- Library fix for Queue/GATK 3.2 · 044fe79f
  Peter van 't Hof authored Jul 18, 2014
  
  044fe79f
15 Jul, 2014 14 commits
- Merge branch 'patch_readme' into 'master' · 398500a6
  Peter van 't Hof authored Jul 15, 2014
```
README updates

README updates with installation notes (includes non-SHARK and SHARK installs)
```
  398500a6
- Update to Queue/GATK 3.2 · 0a33b3d3
  Peter van 't Hof authored Jul 15, 2014
  
  0a33b3d3
- Update README with installation notes · 90bfd70e
  bow authored Jul 15, 2014
  
  90bfd70e
- Summary is skipped in chunking mode · 719894d1
  Peter van 't Hof authored Jul 15, 2014
  
  719894d1
- intial unzipped file is intermediate now · 2e45f064
  Peter van 't Hof authored Jul 15, 2014
  
  2e45f064
- Added a module for Genotyping · 43881d8d
  Peter van 't Hof authored Jul 15, 2014
  
  43881d8d
- Fixed file location when not chunking · 4e925feb
  Peter van 't Hof authored Jul 15, 2014
  
  4e925feb
- Option to skip summary · 9be7a784
  Peter van 't Hof authored Jul 15, 2014
  
  9be7a784
- Added a git ignore · bd29df9d
  Peter van 't Hof authored Jul 15, 2014
  
  bd29df9d
- Added gatk-variantcalling module · 0d280a78
  Peter van 't Hof authored Jul 15, 2014
  
  0d280a78
- Fix outputDir for flexiprep · a2ebfada
  Peter van 't Hof authored Jul 15, 2014
  
  a2ebfada
- Add check on outputDir · 21b032c9
  Peter van 't Hof authored Jul 15, 2014
  
  21b032c9
- Code style fix · d6a28af2
  Peter van 't Hof authored Jul 15, 2014
  
  d6a28af2
- Add QC plot for base recal · 448cb3dd
  Peter van 't Hof authored Jul 15, 2014
  
  448cb3dd
14 Jul, 2014 2 commits
- Changed to a trait · 3cd7b3bf
  Peter van 't Hof authored Jul 14, 2014
  
  3cd7b3bf
- Added variantcalling pipeline based on bam files · c19f372f
  Peter van 't Hof authored Jul 14, 2014
  
  c19f372f
03 Jul, 2014 6 commits
- Indel realign is now intermediate · bb32c1aa
  Peter van 't Hof authored Jul 03, 2014
  
  bb32c1aa
- Test file changes · b42ce554
  Peter van 't Hof authored Jul 03, 2014
  
  b42ce554
- Added configValue2string · 2057747f
  Peter van 't Hof authored Jul 03, 2014
  
  2057747f
- Added bedtools functions · 9aebd092
  Peter van 't Hof authored Jul 03, 2014
  
  9aebd092
- codestyle fix · e626880a
  Peter van 't Hof authored Jul 03, 2014
  
  e626880a
- Added dependency for bam-metrics · 97cf8080
  Peter van 't Hof authored Jul 03, 2014
  
  97cf8080