Commits · d580c130c863c802adb20dce4c6b3930dfc2c8f8 · Thomas Weber / Mosaicatcher Update

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
Dec 08, 2017
- fixed bug in converter of Maryam's probability table · aa4ae7ef
  Sascha Meiers authored 7 years ago
  
  aa4ae7ef
Dec 07, 2017
- Fix installation · 120c8165
  Sascha Meiers authored 7 years ago
  
  120c8165
- Fixes: no spaces after \. no need for . also, add dependency for installation · 37dde887
  Sascha Meiers authored 7 years ago
  
  37dde887
- Removed trash file · 87b65078
  Sascha Meiers authored 7 years ago
  
  87b65078
Dec 04, 2017
- removed class_dir & class_script params · 07479b70
  maryamghr authored 7 years ago
  
  07479b70
- added Maryam to the pipeline · 29767967
  daewoooo authored 7 years ago
  
  29767967
Nov 17, 2017
- dirty hack to remove chrX and chrY · e9e7281c
  Sascha Meiers authored 7 years ago
  
  e9e7281c
Nov 16, 2017
- added gitignore · 2398f57b
  Sascha Meiers authored 7 years ago
  
  2398f57b
- StrandPhaser config file is now dynamically generated · 01149e62
  Sascha Meiers authored 7 years ago
  
  01149e62
- Integrated Strandphaser into Snakemake pipeline. However, Strandphaser still throws an error · bcd95dd8
  Sascha Meiers authored 7 years ago
  
  bcd95dd8
Nov 14, 2017
- Added StrandPhaseR pipeline · 044fd3d7
  daewoooo authored 7 years ago
  
  044fd3d7
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 27, 2017
- Integrate SV classification into pipeline. There are still errors in the SV classification script · 8aa711c6
  Sascha Meiers authored 7 years ago
  
  8aa711c6
Oct 26, 2017
- Fixed more fatal typos. gotta catch 'em all · c29ad663
  Sascha Meiers authored 7 years ago
  
  c29ad663
- Fixed another fatal type · a867aae2
  Sascha Meiers authored 7 years ago
  
  a867aae2
- Added variable-width bins in two window sizes · e25253ae
  Sascha Meiers authored 7 years ago
  
  e25253ae
- Fixed fatal type · 04c66cdb
  Sascha Meiers authored 7 years ago
  
  04c66cdb
- Fix for prev. commit · 0044adb9
  Sascha Meiers authored 7 years ago
  
  0044adb9