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

Oct 23, 2018
- now 8 cores for delly · 24b86bc5
  Thomas Faraut authored 6 years ago
  
  24b86bc5
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
- Remove unused genotyping rule · a2da3720
  Floreal Cabanettes authored 6 years ago
  
  a2da3720
- 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 20, 2018
- Fix chromosomes with no reads for lumpy · 96f3d4d0
  Floreal Cabanettes authored 6 years ago
  
  96f3d4d0
- Fix syntax · 7fd9cbca
  Floreal Cabanettes authored 6 years ago
  
  7fd9cbca
- Try another approach to fix the problem · 76fd6d52
  Floreal Cabanettes authored 6 years ago
  
  76fd6d52
Jul 02, 2018
- Fix syntax · 4079e8ba
  Floreal Cabanettes authored 6 years ago
  
  4079e8ba
- 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
Jun 14, 2018
- Fix typo · b8004357
  Floreal Cabanettes authored 6 years ago
  
  b8004357
- Fix syntax · efb8306f
  Floreal Cabanettes authored 6 years ago
  
  efb8306f
- Multicopy CNVs: sh -> py · efbf8706
  Floreal Cabanettes authored 6 years ago
  
  efbf8706
- Preprocess move to python · 10832e0e
  Floreal Cabanettes authored 6 years ago
  
  10832e0e
- Replace genomestrip sh by a python executor · d87430fb
  Floreal Cabanettes authored 6 years ago
  
  d87430fb
Jun 07, 2018
- Add refbundle workflow to the simulation pipeline · 9452d0d0
  Floreal Cabanettes authored 6 years ago
  
  9452d0d0
May 28, 2018
- added exclude region to pindel · a2fe311f
  Thomas Faraut authored 6 years ago
  
  a2fe311f
May 03, 2018
- bug correction bnd_merge due to duplication of start and en in DellyRecord · 77700be1
  Thomas Faraut authored 6 years ago
  
  77700be1
- Rename CNV variant type mCNV · 90b60dea
  Floreal Cabanettes authored 6 years ago
  
  90b60dea
May 02, 2018
- Fix syntax · cc66a5a0
  Floreal Cabanettes authored 6 years ago
  
  cc66a5a0
- Fix syntax · 953062c4
  Floreal Cabanettes authored 6 years ago
  
  953062c4
- Improve cnv variants output declaration + add logs · 6278c60d
  Floreal Cabanettes authored 6 years ago
  
  6278c60d
- Fix intervallist rule · 4c95b317
  Floreal Cabanettes authored 6 years ago
  
  4c95b317

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