Commits · cc1bf0dedfb7ac596f06e962668ba30a3a57ba21 · Thomas Weber / Mosaicatcher Update · GitLab

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Jun 19, 2018
- Add default VCF files for RPE cell line data · cc1bf0de
  Sascha Meiers authored 6 years ago
  
  cc1bf0de
Jun 17, 2018
- Fixed small typo · 09197f57
  Sascha Meiers authored 6 years ago
  
  09197f57
- Clean up old entries · 1d52cf23
  Sascha Meiers authored 6 years ago
  
  1d52cf23
Jun 15, 2018
- Use more recent SV plot script + do not black list counts based initially · 3ca02902
  Sascha Meiers authored 6 years ago
  
  3ca02902
Jun 14, 2018
- Use more recent version of qc.R · 44c28d26
  Sascha Meiers authored 6 years ago
  
  44c28d26
Jun 12, 2018
- Add new way of normalization (right at the start). Remove old one · f07cf7eb
  Sascha Meiers authored 6 years ago
  
  f07cf7eb
Jun 05, 2018
- removed expectation-level normalization by default · f6123fc7
  Sascha Meiers authored 6 years ago
  
  f6123fc7
Jun 04, 2018
- Include log-likelihood-ratio filter and normalization · c6ab4003
  Sascha Meiers authored 6 years ago
  
  c6ab4003
May 30, 2018
- Added normalization file for 50 kb based on HGSVC trio coverage. Enable 50kb in pipeline · 2b6b6b06
  Sascha Meiers authored 6 years ago
  
  2b6b6b06
May 22, 2018
- adding new SCE classification --> Need to re-install MosaiCatcher C++ code! · 18374424
  Sascha Meiers authored 6 years ago
  
  18374424
May 18, 2018
- Changed the density of segmentation · 54c2cd67
  Sascha Meiers authored 6 years ago
  
  54c2cd67
May 16, 2018
- add new SV plot and prepare Snakefile for new SV classifier · 6335805c
  Sascha Meiers authored 6 years ago
  
  6335805c
Feb 16, 2018
- fixed comma in JSON · 8118a911
  Sascha Meiers authored 7 years ago
  
  8118a911
- New parameters for simulations · 9cd23b43
  Sascha Meiers authored 7 years ago
  
  9cd23b43
Jan 20, 2018
- Fixed re-naming of cells in 'convert_svprob_output'. ALso, plot segmentation for chr1 · 68731952
  Sascha Meiers authored 7 years ago
  
  68731952
Jan 18, 2018
- Paired- or single-end mode for StrandPhasR · 47cc8975
  Sascha Meiers authored 7 years ago
  
  47cc8975
Jan 12, 2018
- Add alpha parameter, use --seed option of mosaic simulate, and create link to... · fd270e1c
  Tobias Marschall authored 7 years ago
  
  Add alpha parameter, use --seed option of mosaic simulate, and create link to simulated strand states
  fd270e1c
- Added rules for simulating counts · c217146a
  Tobias Marschall authored 7 years ago
  
  c217146a
Jan 11, 2018
- Remove sample name from config · 93e64c21
  Sascha Meiers authored 7 years ago
  
  Unverified
  
  93e64c21
- Chromosomes are now specified within the config file. Exclude file is auto-generated · d3008a55
  Sascha Meiers authored 7 years ago
  
  d3008a55
Jan 10, 2018
- Add config option snv_calls to use existing SNV call sets · d580c130
  Tobias Marschall authored 7 years ago
  
  d580c130
- Made R reference (needed in Strand-PhaseR) a config parameter · 701849db
  Sascha Meiers authored 7 years ago
  
  701849db
Dec 04, 2017
- removed class_dir & class_script params · 07479b70
  maryamghr authored 7 years ago
  
  07479b70
Nov 16, 2017
- Integrated Strandphaser into Snakemake pipeline. However, Strandphaser still throws an error · bcd95dd8
  Sascha Meiers authored 7 years ago
  
  bcd95dd8
Oct 30, 2017
- Prepared rules to run SV classification tool, convert its output and plot it · 47125871
  Sascha Meiers authored 7 years ago
  
  47125871
Oct 26, 2017
- new step in the pipeline to prepare input files for calculation of SV propabilities · 216dbac5
  Sascha Meiers authored 7 years ago
  
  216dbac5
- Initial pipeline that does part of the job · 7eb5f6b1
  Sascha Meiers authored 7 years ago
  
  7eb5f6b1