Commits · 384619998536ae934c5ca21ce378becc6e3403b2 · Mirrors / biopet.biopet

Nov 19, 2015
- Sync with develop · 38461999
  Wai Yi Leung authored 9 years ago
  
  38461999
- Fixed bug in loading the mainClass for biopet tools · 7f424eb9
  Peter van 't Hof authored 9 years ago
  
  7f424eb9
Nov 11, 2015
- Add fixme · 2a64a1d6
  Peter van 't Hof authored 9 years ago
  
  2a64a1d6
- Disabled intermediate markduplicates · 364b0d00
  Peter van 't Hof authored 9 years ago
  
  364b0d00
Nov 08, 2015
- Enforce absolute paths for input files · 10524ce8
  Peter van 't Hof authored 9 years ago
  
  10524ce8
Nov 02, 2015
- Style changes · d7a5a9ef
  Peter van 't Hof authored 9 years ago
  
  d7a5a9ef
- Added sunburst plot to mapping and shiva · 89bc7d9a
  Peter van 't Hof authored 9 years ago
  
  89bc7d9a
Oct 29, 2015
- Added bammetrics when start from bam file · ef5ea6ce
  Peter van 't Hof authored 9 years ago
  
  ef5ea6ce
- Hide QC from report when flexiprep is not executed · 3d73d611
  Peter van 't Hof authored 9 years ago
  
  3d73d611
- Fixed link to bai file · 55aba945
  Peter van 't Hof authored 9 years ago
  
  55aba945
Oct 28, 2015
- Added args · ef3b8eb6
  Peter van 't Hof authored 9 years ago
  
  ef3b8eb6
- Style change · 21d64302
  Peter van 't Hof authored 9 years ago
  
  21d64302
- Fixed report · 2483b207
  Peter van 't Hof authored 9 years ago
  
  2483b207
Oct 27, 2015
- fixed missing key · 1a33022a
  Peter van 't Hof authored 9 years ago
  
  1a33022a
- Removed double index · b00a8f2f
  Peter van 't Hof authored 9 years ago
  
  b00a8f2f
- Fix sample flag · 1101daa7
  Peter van 't Hof authored 9 years ago
  
  1101daa7
- Changed file name · 3921c5d9
  Peter van 't Hof authored 9 years ago
  
  3921c5d9
- Fix type · 85735dd3
  Peter van 't Hof authored 9 years ago
  
  85735dd3
- Added input files to summary of shiva · 5448ee58
  Peter van 't Hof authored 9 years ago
  
  5448ee58
- Added more setting to the report · ba50ff98
  Peter van 't Hof authored 9 years ago
  
  ba50ff98
- Hide variant report when multisample variantcalling is not executed · ffd2f2fa
  Peter van 't Hof authored 9 years ago
  
  ffd2f2fa
- Refactor usage of Delly pipeline a bit by adding CatVariants and moving Delly to Shiva · a68e86c1
  Wai Yi Leung authored 9 years ago
  
  a68e86c1
- Added more settings to the summary · ad4b957a
  Peter van 't Hof authored 9 years ago
  
  ad4b957a
- Remove undeed trait · 59e750bf
  Peter van 't Hof authored 9 years ago
  
  59e750bf
Oct 26, 2015
- Fix summary key · 186db74d
  Peter van 't Hof authored 9 years ago
  
  186db74d
- Fixed bcftools merge step · 779e8aa3
  Peter van 't Hof authored 9 years ago
  
  779e8aa3
Oct 23, 2015
- Added GenotypeConcordance to shiva · 18e22c1b
  Peter van 't Hof authored 9 years ago
  
  18e22c1b
Oct 21, 2015
- Change to compressed output · 46f8b1b5
  Peter van 't Hof authored 9 years ago
  
  46f8b1b5
- Fix sample and library flag · 43a4bc76
  Peter van 't Hof authored 9 years ago
  
  43a4bc76
- changed imports · 0d010c88
  Sander van der Zeeuw authored 9 years ago
  
  0d010c88
Oct 20, 2015
- Fix flag · fe91eb82
  Peter van 't Hof authored 9 years ago
  
  fe91eb82
- added bcftools singlesample to the test of public · 025740f5
  Sander van der Zeeuw authored 9 years ago
  
  025740f5
Oct 19, 2015
- added dependency for combinevariants · f17e2175
  Sander van der Zeeuw authored 9 years ago
  
  f17e2175
Oct 16, 2015
- add bcf merge to shiva and create wrapper · 34024cc5
  Sander van der Zeeuw authored 9 years ago
  
  34024cc5
- added tabix to bcftools output · f1599432
  Sander van der Zeeuw authored 9 years ago
  
  f1599432
Oct 15, 2015
- added proper piping to bcftools and mpileup. [GENTRAP VARSCAN SHOULD BE TESTED] · 76da8883
  Sander van der Zeeuw authored 9 years ago
  
  76da8883
- Remove "reference" from testing · f4fb8907
  Peter van 't Hof authored 9 years ago
  
  (cherry picked from commit 8bf162ad)
  f4fb8907
- Remove "reference" from testing · 8bf162ad
  Peter van 't Hof authored 9 years ago
  
  8bf162ad
- added bcftools_singlesample · 695ef882
  Sander van der Zeeuw authored 9 years ago
  
  695ef882
Oct 12, 2015
- mpileup_reference_added · a6e9c469
  Sander van der Zeeuw authored 9 years ago
  
  a6e9c469