Commits · 3d66929f30f054a417f712cf8def93e44208d342 · SVdetection / cnvpipelines

Aug 13, 2019
- SnekamakeCommand py --> smk · 3d66929f
  Thomas Faraut authored 5 years ago
  
  3d66929f
- working align smk · 13e356e9
  Thomas Faraut authored 5 years ago
  
  13e356e9
- new factorization · 7dadb6ec
  Thomas Faraut authored 5 years ago and Thomas Faraut committed 5 years ago
  
  7dadb6ec
Jul 23, 2019
- specifying a correct place for conda envs · 60588422
  Thomas Faraut authored 5 years ago
  
  60588422
- fixing svtyper env for mergebatch · 0bdb7b05
  Thomas Faraut authored 5 years ago
  
  0bdb7b05
Jul 22, 2019
- bug correction in genomestrip bwa index · 9665ca36
  Thomas Faraut authored 5 years ago
  
  9665ca36
- new factorization · 567b4f59
  Thomas Faraut authored 5 years ago
  
  567b4f59
Jul 11, 2019
- adding vcf-sort · dfc14d5d
  Thomas Faraut authored 5 years ago
  
  dfc14d5d
- a functional version · 94a7830d
  Thomas Faraut authored 5 years ago
  
  94a7830d
- fix LD_LIBRARY_PATH · 812ed80f
  Thomas Faraut authored 5 years ago
  
  812ed80f
- bwa execution mode · 8d0ca0fc
  Thomas Faraut authored 5 years ago
  
  8d0ca0fc
Jul 10, 2019
- adding vcf-sort · b4093cf9
  Thomas Faraut authored 5 years ago
  
  b4093cf9
- use conda delly · 23ef70cc
  Thomas Faraut authored 5 years ago
  
  23ef70cc
- removing link for referencebundle · 9300b44a
  Thomas Faraut authored 5 years ago
  
  9300b44a
- new complete install · 23152661
  Thomas Faraut authored 5 years ago
  
  23152661
Jul 09, 2019
- updating svlib · d0905550
  Thomas Faraut authored 5 years ago
  
  d0905550
- updating lib · 02462ca4
  Thomas Faraut authored 5 years ago
  
  02462ca4
- updating lib · 98b8440e
  Thomas Faraut authored 5 years ago
  
  98b8440e
- updating lib · 944249bf
  Thomas Faraut authored 5 years ago
  
  944249bf
- installing genomestrip using conda · 262743e3
  Thomas Faraut authored 5 years ago
  
  262743e3
Jul 08, 2019
- new installation procedure · b5c5e280
  Thomas Faraut authored 5 years ago
  
  b5c5e280
Jul 05, 2019
- buid_pop -> build_variant_pop · c3548d4d
  Thomas Faraut authored 5 years ago
  
  c3548d4d
Jul 03, 2019
- some memory and trhead parameter reconfiguration · dc3fc525
  Thomas Faraut authored 5 years ago
  
  dc3fc525
May 27, 2019
- some comestic changes · e8d91743
  Thomas Faraut authored 5 years ago
  
  e8d91743
- some more explicit messages. Correcting positions for gaps · 8c8bba97
  Thomas Faraut authored 5 years ago
  
  8c8bba97
Feb 15, 2019
- Updating lib · f9dacd58
  Thomas Faraut authored 6 years ago
  
  f9dacd58
Feb 05, 2019
- Duplication support in simulation;Creation of the sample.list containing all... · c1c72ff8
  Mathieu Charles authored 6 years ago
  
  Duplication support in simulation;Creation of the sample.list containing all samples, additionnaly to sample.list.# for batch
  c1c72ff8
Jan 17, 2019
- bwam in cluster.yaml set to 23h, detect_region_to_exclude modified · 9fe53a17
  Thomas Faraut authored 6 years ago
  
  9fe53a17
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 05, 2018
- removing izip and pysamstats import · e6a8ad6a
  Thomas Faraut authored 6 years ago
  
  e6a8ad6a
Dec 04, 2018
- - delly ex is now mine · 5225e199
  Thomas Faraut authored 6 years ago
  
  - get_regions to exclude uses not mad
  5225e199
- - 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
- upgrading lib · b0c65c57
  Thomas Faraut authored 6 years ago
  
  b0c65c57
Oct 23, 2018
- now 8 cores for delly · 24b86bc5
  Thomas Faraut authored 6 years ago
  
  24b86bc5
- removing self._rerun_tools(tools) · b4182d5e
  Thomas Faraut authored 6 years ago
  
  b4182d5e
Oct 19, 2018
- adding batch id to record id in parse · 9408978e
  Thomas Faraut authored 6 years ago
  
  9408978e
- updating snakecnv/lib · fc048fbe
  Thomas Faraut authored 6 years ago
  
  fc048fbe
Oct 05, 2018
- patch for getting chromsomes in get_batches · 272bf2f3
  Thomas Faraut authored 6 years ago
  
  272bf2f3
Sep 27, 2018
- updating the lib submodule · 491fa286
  Thomas Faraut authored 6 years ago
  
  491fa286
- - 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