Commits · 8d17bcbb2933c2c79712526abe256a1f21470b37 · Mirrors / biopet.biopet

12 Sep, 2014 4 commits
- Add output_mode option · 8d17bcbb
  Peter van 't Hof authored Sep 12, 2014
  
  8d17bcbb
- Added joint variantcalling step · a5616824
  Peter van 't Hof authored Sep 12, 2014
  
  a5616824
- Function for gvcf mode · 8820b625
  Peter van 't Hof authored Sep 12, 2014
  
  8820b625
- Changed multisample trait · 7772e165
  Peter van 't Hof authored Sep 12, 2014
  
  7772e165
11 Sep, 2014 4 commits
- Changed multisample trait · 348a42c4
  Peter van 't Hof authored Sep 11, 2014
  
  348a42c4
- Fir doublePreProces · 6b28d218
  Peter van 't Hof authored Sep 11, 2014
  
  6b28d218
- Changed default stand_call_conf · c3a86435
  Peter van 't Hof authored Sep 11, 2014
  
  c3a86435
- Changed output file to .gz · 47c4429a
  Peter van 't Hof authored Sep 11, 2014
  
  47c4429a
10 Sep, 2014 6 commits
- New version · 7b6e8c6e
  Peter van 't Hof authored Sep 10, 2014
  
  7b6e8c6e
- Moved all to afterGraph function · 61695e0a
  Peter van 't Hof authored Sep 10, 2014
  
  61695e0a
- Fix default map · 96b4f7a0
  Peter van 't Hof authored Sep 10, 2014
  
  96b4f7a0
- Added combineVariants step · 3515b72a
  Peter van 't Hof authored Sep 10, 2014
  
  3515b72a
- Fix multiple issues · 7551158a
  Peter van 't Hof authored Sep 10, 2014
  
  7551158a
- Added index as output file · 5118a46c
  Peter van 't Hof authored Sep 10, 2014
  
  5118a46c
09 Sep, 2014 13 commits
- Fix on correct readgroup · 1f5eaf15
  Peter van 't Hof authored Sep 09, 2014
  
  1f5eaf15
- Fix on bam input · 07aa62d7
  Peter van 't Hof authored Sep 09, 2014
  
  07aa62d7
- put all back because breaking some gatk modules · f75d3b63
  Peter van 't Hof authored Sep 09, 2014
  
  f75d3b63
- fix any2list function · f205d023
  Peter van 't Hof authored Sep 09, 2014
  
  f205d023
- Fix interval passing · 370cd1ad
  Peter van 't Hof authored Sep 09, 2014
  
  370cd1ad
- Fix on readgroup items · 6309b412
  Peter van 't Hof authored Sep 09, 2014
  
  6309b412
- Added support for bam files as input for pipeline · 5ca82acf
  Peter van 't Hof authored Sep 09, 2014
  
  5ca82acf
- Fix default aligner in constructor · 849188d8
  Peter van 't Hof authored Sep 09, 2014
  
  849188d8
- Added option for metrics for each chunk · 71b12276
  Peter van 't Hof authored Sep 09, 2014
  
  71b12276
- Now can use piped command from samtools · c43bfa2a
  Peter van 't Hof authored Sep 09, 2014
  
  c43bfa2a
- Added samtools modules · b5461f9d
  Peter van 't Hof authored Sep 09, 2014
  
  b5461f9d
- More concise code · 5af4086c
  Peter van 't Hof authored Sep 09, 2014
  
  5af4086c
- Exe no freeVar anymore · 52d84e3c
  Peter van 't Hof authored Sep 09, 2014
  
  52d84e3c
08 Sep, 2014 8 commits
- Add mpileup to vcf script · 9cfacde5
  Peter van 't Hof authored Sep 08, 2014
  
  9cfacde5
- Added target_bed as default to the intervals for all gatk functions · 34153b63
  Peter van 't Hof authored Sep 08, 2014
  
  34153b63
- Added gatk as sumodule for all general options · ec3a1894
  Peter van 't Hof authored Sep 08, 2014
  
  ec3a1894
- Added defaults to the contains function · 7e5a520e
  Peter van 't Hof authored Sep 08, 2014
  
  7e5a520e
- Config name change · 0b455f08
  Peter van 't Hof authored Sep 08, 2014
  
  0b455f08
- More efficient code · 8df9dd6a
  Peter van 't Hof authored Sep 08, 2014
  
  8df9dd6a
- Last bam file not intermediate anymore · abb2a682
  Peter van 't Hof authored Sep 08, 2014
  
  abb2a682
- Fixed chunking output dirs · c2284b8b
  Peter van 't Hof authored Sep 08, 2014
  
  c2284b8b
05 Sep, 2014 2 commits
- Added variant recalibration as separated pipeline · a827c3b4
  Peter van 't Hof authored Sep 05, 2014
  
  a827c3b4
- Give all gatk function there own class · 8685e51a
  Peter van 't Hof authored Sep 05, 2014
  
  8685e51a
03 Sep, 2014 3 commits
- Added a general biopet trait for gatk extensions · 83c9a8e5
  Peter van 't Hof authored Sep 03, 2014
  
  83c9a8e5
- Added getFileList function · e323ae4c
  Peter van 't Hof authored Sep 03, 2014
  
  e323ae4c
- Moved samples to single root directory · 9e5781c3
  Peter van 't Hof authored Sep 03, 2014
  
  9e5781c3