Commits · c217146aecfd6c4cf4421ae0008b8b25194f4cf1 · Thomas Weber / Mosaicatcher Update · GitLab

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Jan 12, 2018
- Added rules for simulating counts · c217146a
  Tobias Marschall authored 7 years ago
  
  c217146a
- Merge branch 'master' of https://github.com/friendsofstrandseq/pipeline · d93cb38d
  Sascha Meiers authored 7 years ago
  
  d93cb38d
- overwriting with correct version + fixing library loading · f5dc7a31
  Sascha Meiers authored 7 years ago
  
  f5dc7a31
Jan 11, 2018
- Added rule to simulate a genome · 56992d29
  Tobias Marschall authored 7 years ago
  
  56992d29
- Expose parameters to command line, add random seed, sample size log-uniformly. · 99153c9e
  Tobias Marschall authored 7 years ago
  
  99153c9e
- Copied simulation script from strandsequtils/simulation_for_maryam/simulate_SVs.R · 76c9b592
  Tobias Marschall authored 7 years ago
  
  76c9b592
- Adapted StrandPhaseR's output path · f227a86d
  Sascha Meiers authored 7 years ago
  
  f227a86d
- Remove sample name from config · 93e64c21
  Sascha Meiers authored 7 years ago
  
  Unverified
  
  93e64c21
- Fixing usage of wildcards · 4538c902
  Sascha Meiers authored 7 years ago
  
  4538c902
- fix · 15c4b0a0
  Sascha Meiers authored 7 years ago
  
  15c4b0a0
- Require external VCF to be zipped and indexed · f7fa6c66
  Sascha Meiers authored 7 years ago
  
  f7fa6c66
- Explain that multiple samples can be run now · b56d81f0
  Sascha Meiers authored 7 years ago
  
  b56d81f0
- small fixes · 38ec6a6d
  Sascha Meiers authored 7 years ago
  
  38ec6a6d
- First attempt at parallelizing samples ! · aff42f7e
  Sascha Meiers authored 7 years ago
  
  aff42f7e
- Chromosomes are now specified within the config file. Exclude file is auto-generated · d3008a55
  Sascha Meiers authored 7 years ago
  
  d3008a55
- whitespaces · 2c3fe3ee
  Sascha Meiers authored 7 years ago
  
  2c3fe3ee
- Merge branch 'master' of https://github.com/friendsofstrandseq/pipeline · 0887883f
  Sascha Meiers authored 7 years ago
  
  0887883f
- Fix pipefail error when merging StrandphaseR output · 0bf3f2a5
  Sascha Meiers authored 7 years ago
  
  0bf3f2a5
Jan 10, 2018
- Add config option snv_calls to use existing SNV call sets · d580c130
  Tobias Marschall authored 7 years ago
  
  d580c130
- Mention BSgenome.Hsapiens.UCSC.hg38 · 7947b787
  Tobias Marschall authored 7 years ago
  
  7947b787
- small fix · 27de5e66
  Sascha Meiers authored 7 years ago
  
  27de5e66
- Merge branch 'master' of https://github.com/friendsofstrandseq/pipeline · fe6e7285
  Sascha Meiers authored 7 years ago
  
  fe6e7285
- Made R reference (needed in Strand-PhaseR) a config parameter · 701849db
  Sascha Meiers authored 7 years ago
  
  701849db
- caution: hardcoded Chrom (merged) · d4735d59
  Sascha Meiers authored 7 years ago
  
  d4735d59
- Fixing issues with SV_plot script · d1bf6689
  Sascha Meiers authored 7 years ago
  
  d1bf6689
- CAUTION: hard-coding of chromosome. · fc323de9
  Sascha Meiers authored 7 years ago
  
  TODO: a dynamic rule for chromosomes would be more elegant here, but I have trouble getting it to work
  fc323de9
- Removed variable-width bins from the pipeline for now · 18ff2e6a
  Sascha Meiers authored 7 years ago
  
  TODO: add them again
  18ff2e6a
- Parallelized StrandphasR · 2f234895
  Sascha Meiers authored 7 years ago
  
  2f234895
- Reverted previous attempt for parallelization · 0fc2677c
  Sascha Meiers authored 7 years ago
  
  0fc2677c
- Belongs to previous commit · 162a8139
  Sascha Meiers authored 7 years ago
  
  162a8139
- Parallel mode of StrandPhaseR · 2dbd4da6
  Sascha Meiers authored 7 years ago
  
  2dbd4da6
Dec 22, 2017
- Remove temporary vcf files · 494dc2aa
  Sascha Meiers authored 7 years ago
  
  494dc2aa
Dec 21, 2017
- Fixed log file · 0b45cbf3
  Sascha Meiers authored 7 years ago
  
  0b45cbf3
- fixed empty snv calls · 409c7ecb
  Sascha Meiers authored 7 years ago
  
  409c7ecb
Dec 20, 2017
- Merge branch 'master' of https://github.com/friendsofstrandseq/pipeline · 1073911b
  Sascha Meiers authored 7 years ago
  
  1073911b
- added filtering step to bcftools SNV calling · 81eb3cde
  dporubsky authored 7 years ago
  
  Unverified
  
  81eb3cde
Dec 13, 2017
- More LOG messages · a46a4107
  Sascha Meiers authored 7 years ago
  
  a46a4107
Dec 12, 2017
- Added more numbers of segments · 07d8af42
  Sascha Meiers authored 7 years ago
  
  07d8af42
Dec 11, 2017
- Fixed installation of MaRyam · 34c07afb
  Sascha Meiers authored 7 years ago
  
  34c07afb
- Fixed hardcoded sample name · 740c63ec
  Sascha Meiers authored 7 years ago
  
  740c63ec