Commits · 3d9362820b2907c010d0aef59465a8ab2920af59 · Mirrors / biopet.biopet

22 Sep, 2014 4 commits
- Remove unused lines · 3d936282
  Peter van 't Hof authored Sep 22, 2014
  
  3d936282
- Added filter step · 22b4b757
  Peter van 't Hof authored Sep 22, 2014
  
  22b4b757
- Now outputs a multi allelic vcf file · f0fd2b99
  Peter van 't Hof authored Sep 22, 2014
  
  f0fd2b99
- Fix config name space · 4c3b9198
  Peter van 't Hof authored Sep 22, 2014
  
  4c3b9198
17 Sep, 2014 2 commits
- Added overlap metrics plot · f49a3ad8
  Peter van 't Hof authored Sep 17, 2014
  
  f49a3ad8
- Output files change to gz output · 03325266
  Peter van 't Hof authored Sep 17, 2014
  
  03325266
16 Sep, 2014 1 commit
- Added known option · 168c2d80
  Peter van 't Hof authored Sep 16, 2014
  
  168c2d80
15 Sep, 2014 2 commits
- Fix counting on big files · 5f8092e9
  Peter van 't Hof authored Sep 15, 2014
  
  5f8092e9
- Joint variantcalling is now optional · b36a4b5e
  Peter van 't Hof authored Sep 15, 2014
  
  b36a4b5e
12 Sep, 2014 9 commits
- Changed test files · 73f8e468
  Peter van 't Hof authored Sep 12, 2014
  
  73f8e468
- Added combine multisample variantcalling · c1748449
  Peter van 't Hof authored Sep 12, 2014
  
  c1748449
- Change to sample field · 3eb548bd
  Peter van 't Hof authored Sep 12, 2014
  
  3eb548bd
- Change to biopet gatk modules · fbf778ac
  Peter van 't Hof authored Sep 12, 2014
  
  fbf778ac
- Added CombineVariants · 70b36acd
  Peter van 't Hof authored Sep 12, 2014
  
  70b36acd
- 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 12 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