Commits · 0a33b3d3b71d4905d930b3dd21242ded1a645041 · Mirrors / biopet.biopet

15 Jul, 2014 12 commits
- Update to Queue/GATK 3.2 · 0a33b3d3
  Peter van 't Hof authored Jul 15, 2014
  
  0a33b3d3
- 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 18 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
- Added dependency for bam-metrics · 7b56eb38
  Peter van 't Hof authored Jul 03, 2014
  
  7b56eb38
- Switched to biopet markduplicates · 349330de
  Peter van 't Hof authored Jul 03, 2014
  
  349330de
- Switched to biopet markduplicates · 9add492d
  Peter van 't Hof authored Jul 03, 2014
  
  9add492d
- First version of working bam-metrics pipeline · 97327078
  Peter van 't Hof authored Jul 03, 2014
  
  97327078
- Added default vmem · 801ac09e
  Peter van 't Hof authored Jul 03, 2014
  
  801ac09e
- Disabled command to report for java jobs · 4b5b6c56
  Peter van 't Hof authored Jul 03, 2014
  
  4b5b6c56
- changed version command to def · ddfac817
  Peter van 't Hof authored Jul 03, 2014
  
  ddfac817
- changed version command to def · c340b559
  Peter van 't Hof authored Jul 03, 2014
  
  c340b559
- Added BiopetFlagstat · 07c486e9
  Peter van 't Hof authored Jul 03, 2014
  
  07c486e9
- Added script for bed to picard interval file · cfe60c25
  Peter van 't Hof authored Jul 03, 2014
  
  cfe60c25
- Added samtools flagstat · 83b6e834
  Peter van 't Hof authored Jul 03, 2014
  
  83b6e834
- Added some picard tools to biopet · fcaea52d
  Peter van 't Hof authored Jul 03, 2014
  
  fcaea52d
27 Jun, 2014 8 commits
- Removed argonaut · 4deb4b69
  Peter van 't Hof authored Jun 27, 2014
  
  4deb4b69
- Added pipeline template · 102d3f50
  Peter van 't Hof authored Jun 27, 2014
  
  102d3f50
- Added pipeline template · 61f20583
  Peter van 't Hof authored Jun 27, 2014
  
  61f20583
- Added empty pipeline for bam metrics · 7cad5b3f
  Peter van 't Hof authored Jun 27, 2014
  
  7cad5b3f
- Added dependency · e1490bad
  Peter van 't Hof authored Jun 27, 2014
  
  e1490bad
- fix analysisName on Ln · 27db54a8
  Peter van 't Hof authored Jun 27, 2014
  
  27db54a8
- Remove unused import · cafd9cd7
  Peter van 't Hof authored Jun 27, 2014
  
  cafd9cd7
- Added chunking for mapping · b7690fca
  Peter van 't Hof authored Jun 27, 2014
  
  b7690fca