Commits · fd66bc96ab384280c3c247f845d6461c18f537e2 · SVdetection / cnvpipelines

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 19, 2018
- adding batch id to record id in parse · 9408978e
  Thomas Faraut authored 6 years ago
  
  9408978e
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 08, 2018
- Fix windows · 0cb9738e
  Floreal Cabanettes authored 6 years ago
  
  0cb9738e
- Change pindel window size to 10M with a overlap change from 100K to 50K · 3fb68ce8
  Floreal Cabanettes authored 6 years ago
  
  3fb68ce8
Aug 06, 2018
- Fix for simulation · b9b0bf11
  Floreal Cabanettes authored 6 years ago
  
  b9b0bf11
- Fix typo · cfc46d52
  Floreal Cabanettes authored 6 years ago
  
  cfc46d52
- Split pindel staff by regions · 7520fbc3
  Floreal Cabanettes authored 6 years ago
  
  7520fbc3
Jul 30, 2018
- Remove nstretch file from popsim parameters · a4599c24
  Floreal Cabanettes authored 6 years ago
  
  a4599c24
Jul 20, 2018
- Try another approach to fix the problem · 76fd6d52
  Floreal Cabanettes authored 6 years ago
  
  76fd6d52
Jul 19, 2018
- Fix reference : use absolute path · 29cd4f16
  Floreal Cabanettes authored 6 years ago
  
  29cd4f16
Jul 04, 2018
- nstrech bug corrected · 8b7c6c80
  Thomas Faraut authored 6 years ago
  
  8b7c6c80
- Fix nstretches rule · a236335e
  Floreal Cabanettes authored 6 years ago
  
  a236335e
Jul 03, 2018
- Change chromosomes filter: filter by size · cd6f17e8
  Floreal Cabanettes authored 6 years ago
  
  cd6f17e8
Jul 02, 2018
- Fix snakefile: all rule must be the first one · edb8011d
  Floreal Cabanettes authored 6 years ago
  
  edb8011d
- Fix syntax · 0a31c6e4
  Floreal Cabanettes authored 6 years ago
  
  0a31c6e4
- Fix rule name · e657038c
  Floreal Cabanettes authored 6 years ago
  
  e657038c
- Index reference genome if not already exists · 86e214c6
  Floreal Cabanettes authored 6 years ago
  
  86e214c6
Jun 07, 2018
- Add refbundle workflow to the simulation pipeline · 9452d0d0
  Floreal Cabanettes authored 6 years ago
  
  9452d0d0
- Add detection workflow to the simulation pipeline · afbac7cc
  Floreal Cabanettes authored 6 years ago
  
  afbac7cc
May 28, 2018
- Move sequential batches recipes to the wrapper · b580d4fe
  Floreal Cabanettes authored 6 years ago
  
  b580d4fe
- Fix PEP8 · 420ca383
  Floreal Cabanettes authored 6 years ago
  
  420ca383
- Fix get_batch_groups function · 4b66b6f9
  Floreal Cabanettes authored 6 years ago
  
  4b66b6f9
- Add sequential batches · 81720a4d
  Floreal Cabanettes authored 6 years ago
  
  81720a4d
May 24, 2018
- making sure that the first bal is indexed before looking for regions to exclude · 4d8809c8
  Thomas Faraut authored 6 years ago
  
  4d8809c8
May 18, 2018
- Fix missing renames · 8530c91c
  Floreal Cabanettes authored 6 years ago
  
  8530c91c
May 03, 2018
- Rename CNV variant type mCNV · 90b60dea
  Floreal Cabanettes authored 6 years ago
  
  90b60dea
May 02, 2018
- Improve cnv variants output declaration + add logs · 6278c60d
  Floreal Cabanettes authored 6 years ago
  
  6278c60d
- Fix snakefile syntax · 1ff23db0
  Floreal Cabanettes authored 6 years ago
  
  1ff23db0
- Fix all rules for CNV type · 84896b4d
  Floreal Cabanettes authored 6 years ago
  
  84896b4d
- Fix all rules for CNV type · f7314bd6
  Floreal Cabanettes authored 6 years ago
  
  f7314bd6
- Add CNV variant type + add option to choose which variant types to detect + refactoring · ae5b445a
  Floreal Cabanettes authored 6 years ago
  
  ae5b445a
Apr 23, 2018
- simply modifying threads and mem for rule infex, and threads for excluded and nstretches · 25a58317
  Thomas Faraut authored 6 years ago
  
  25a58317
Apr 19, 2018
- Fix keywords · d24daf79
  Floreal Cabanettes authored 6 years ago
  
  d24daf79
- Add logs · 273dbb3d
  Floreal Cabanettes authored 6 years ago
  
  273dbb3d
- Fix delly and parse rules · 1ed9bf29
  Floreal Cabanettes authored 6 years ago
  
  1ed9bf29
- Fix delly if no variants found + fix refbundle · 40d2bd34
  Floreal Cabanettes authored 6 years ago
  
  40d2bd34
- Replace all scripts in rules by shells · 03408b06
  Floreal Cabanettes authored 6 years ago
  
  03408b06
- Restore get_first_bam function, removed by a bad merge · 8914f406
  Floreal Cabanettes authored 6 years ago
  
  8914f406
Apr 18, 2018
- adding svtype DUP · aeed36c4
  Thomas Faraut authored 6 years ago
  
  aeed36c4

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