Commits · 9b50863bc1f20158445a4164ef98250e19bcdfe9 · SVdetection / cnvpipelines

Dec 12, 2018
- - pindel back to --max_range_index 3 · 9b50863b
  Thomas Faraut authored 6 years ago
  
  - gstrip_preprocess now requires 16Gb of memory
  9b50863b
Dec 04, 2018

- delly threads downgraded to 6 · fd66bc96

Thomas Faraut authored 6 years ago

- genomestrip .Nstrech file not any more required
- pindel max_xrange 2 removed
- excluded is now preformed for each sample

fd66bc96

Sep 27, 2018
- - implementing a pure pysam bacoverage instead of the pysamstats implementation · cd6a9624
  Thomas Faraut authored 6 years ago
  
  - window width for the detection of high coverage is now 500bp - simplifying gzip of pindel files
  cd6a9624
Aug 06, 2018
- Fix typo · 3fc63cf8
  Floreal Cabanettes authored 6 years ago
  
  3fc63cf8
- Fix pindel command · efb63afe
  Floreal Cabanettes authored 6 years ago
  
  efb63afe
- Make command much readable · cd9d7c85
  Floreal Cabanettes authored 6 years ago
  
  cd9d7c85
- Remove bad wildcard · 3814f78e
  Floreal Cabanettes authored 6 years ago
  
  3814f78e
- Remove bad wildcard · f7544daa
  Floreal Cabanettes authored 6 years ago
  
  f7544daa
- Fix: pindel detect all variants type grouped · 16f1c496
  Floreal Cabanettes authored 6 years ago
  
  16f1c496
- Fix folder name · ae98056b
  Floreal Cabanettes authored 6 years ago
  
  ae98056b
- Pindel windows: place in a subdir, remove subdir after merge · dea55fc2
  Floreal Cabanettes authored 6 years ago
  
  dea55fc2
- Move windowed files in subdir for pindel (try fixing problem...) · 89eba335
  Floreal Cabanettes authored 6 years ago
  
  89eba335
- Fix log filenames · 4a1cfad1
  Floreal Cabanettes authored 6 years ago
  
  4a1cfad1
- Add logs · 94947ee1
  Floreal Cabanettes authored 6 years ago
  
  94947ee1
- Try fix: move script in file and run it with shell · 9705f19b
  Floreal Cabanettes authored 6 years ago
  
  9705f19b
- Revert "Fix pindel command" · 640474a5
  Floreal Cabanettes authored 6 years ago
  
  This reverts commit f5639d2d.
  640474a5
- Fix pindel command · 5c75940b
  Floreal Cabanettes authored 6 years ago
  
  5c75940b
- Use regions in pindel command · da35bb3f
  Floreal Cabanettes authored 6 years ago
  
  da35bb3f
- Split pindel staff by regions · 7520fbc3
  Floreal Cabanettes authored 6 years ago
  
  7520fbc3
Jul 02, 2018
- Fix syntax + fix config · 06b14893
  Floreal Cabanettes authored 6 years ago
  
  06b14893
- Index reference genome if not already exists · 86e214c6
  Floreal Cabanettes authored 6 years ago
  
  86e214c6
May 28, 2018
- added exclude region to pindel · a2fe311f
  Thomas Faraut authored 6 years ago
  
  a2fe311f
Apr 19, 2018
- Fix pindel missing output file · 54e68424
  Floreal Cabanettes authored 6 years ago
  
  54e68424
Apr 18, 2018
- adding svtype DUP · aeed36c4
  Thomas Faraut authored 6 years ago
  
  aeed36c4
Apr 17, 2018
- inversion de la hierarchie des normes · 4020a8fc
  Thomas Faraut authored 6 years ago
  
  4020a8fc
- completed conflict resolve after merge from master · 2f61fa7b
  Thomas Faraut authored 6 years ago
  
  2f61fa7b
Apr 11, 2018
- fixing stdout and stderr for delly and lumpy and other details · 22f3bb62
  Thomas Faraut authored 6 years ago
  
  22f3bb62
Apr 09, 2018
- adding filtered bed and some bug correction · d9b2654c
  Thomas Faraut authored 6 years ago
  
  d9b2654c
Apr 08, 2018
- removing extraction · b23f51b5
  Thomas Faraut authored 6 years ago
  
  b23f51b5
Mar 21, 2018
- Fix batch in pindel · 4c83e3e3
  Floreal Cabanettes authored 7 years ago
  
  4c83e3e3
Mar 20, 2018
- Fix pindel statfile rule · f75ffa66
  Floreal Cabanettes authored 7 years ago
  
  f75ffa66
- Fix batches · fdb6baf1
  Floreal Cabanettes authored 7 years ago
  
  fdb6baf1
- Change batch definition · 7f9edbd3
  Floreal Cabanettes authored 7 years ago
  
  7f9edbd3
- Add batches to pindel and lumpy · 5386867b
  Floreal Cabanettes authored 7 years ago
  
  5386867b
- bug correction · 177d0cdf
  Thomas Faraut authored 7 years ago
  
  177d0cdf
Mar 19, 2018
- - extracted bam files as temp files · 08b97951
  Thomas Faraut authored 7 years ago
  
  - pindel uses now the complete bam files (ie in data/bams)
  08b97951
Mar 16, 2018
- cleaned python modules, removed unnecessary import · 181f1581
  Thomas Faraut authored 7 years ago
  
  181f1581
Mar 13, 2018
- Add inversions svtype to the workflow · fca4b348
  Floreal Cabanettes authored 7 years ago
  
  fca4b348
Mar 09, 2018
- Load number of threads from cluster config if available · 4aaba3a4
  Floreal Cabanettes authored 7 years ago
  
  4aaba3a4
Mar 06, 2018
- Compute insert length without breakdancer · d9f26a47
  Floreal Cabanettes authored 7 years ago
  
  d9f26a47

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