Commits · ea95c71d4d306aa029d0f044e6eacf8756060143 · Mirrors / biopet.biopet

Jul 18, 2014
- Added a benchmark pipeline for gvcf · ea95c71d
  Peter van 't Hof authored 10 years ago
  
  ea95c71d
- Added GatkPipeline, finaly replacement for "Gatk" pipeline · f49e6275
  Peter van 't Hof authored 10 years ago
  
  f49e6275
- Added min_mapping_quality_score to haplotypecaller · ae952d4c
  Peter van 't Hof authored 10 years ago
  
  ae952d4c
- update for Queue/GATK 3.2-2 · 62ed4c90
  Peter van 't Hof authored 10 years ago
  
  62ed4c90
- update for Queue/GATK 3.2-2 · 3b0a7242
  Peter van 't Hof authored 10 years ago
  
  3b0a7242
- Library fix for Queue/GATK 3.2 · 044fe79f
  Peter van 't Hof authored 10 years ago
  
  044fe79f
Jul 15, 2014
- Merge branch 'patch_readme' into 'master' · 398500a6
  Peter van 't Hof authored 10 years ago
  
  README updates README updates with installation notes (includes non-SHARK and SHARK installs)
  398500a6
- Update to Queue/GATK 3.2 · 0a33b3d3
  Peter van 't Hof authored 10 years ago
  
  0a33b3d3
- Update README with installation notes · 90bfd70e
  bow authored 10 years ago
  
  90bfd70e
- Summary is skipped in chunking mode · 719894d1
  Peter van 't Hof authored 10 years ago
  
  719894d1
- intial unzipped file is intermediate now · 2e45f064
  Peter van 't Hof authored 10 years ago
  
  2e45f064
- Added a module for Genotyping · 43881d8d
  Peter van 't Hof authored 10 years ago
  
  43881d8d
- Fixed file location when not chunking · 4e925feb
  Peter van 't Hof authored 10 years ago
  
  4e925feb
- Option to skip summary · 9be7a784
  Peter van 't Hof authored 10 years ago
  
  9be7a784
- Added a git ignore · bd29df9d
  Peter van 't Hof authored 10 years ago
  
  bd29df9d
- Added gatk-variantcalling module · 0d280a78
  Peter van 't Hof authored 10 years ago
  
  0d280a78
- Fix outputDir for flexiprep · a2ebfada
  Peter van 't Hof authored 10 years ago
  
  a2ebfada
- Add check on outputDir · 21b032c9
  Peter van 't Hof authored 10 years ago
  
  21b032c9
- Code style fix · d6a28af2
  Peter van 't Hof authored 10 years ago
  
  d6a28af2
- Add QC plot for base recal · 448cb3dd
  Peter van 't Hof authored 10 years ago
  
  448cb3dd
Jul 14, 2014
- Changed to a trait · 3cd7b3bf
  Peter van 't Hof authored 10 years ago
  
  3cd7b3bf
- Added variantcalling pipeline based on bam files · c19f372f
  Peter van 't Hof authored 10 years ago
  
  c19f372f
Jul 03, 2014
- Indel realign is now intermediate · bb32c1aa
  Peter van 't Hof authored 10 years ago
  
  bb32c1aa
- Test file changes · b42ce554
  Peter van 't Hof authored 10 years ago
  
  b42ce554
- Added configValue2string · 2057747f
  Peter van 't Hof authored 10 years ago
  
  2057747f
- Added bedtools functions · 9aebd092
  Peter van 't Hof authored 10 years ago
  
  9aebd092
- codestyle fix · e626880a
  Peter van 't Hof authored 10 years ago
  
  e626880a
- Added dependency for bam-metrics · 97cf8080
  Peter van 't Hof authored 10 years ago
  
  97cf8080
- Added dependency for bam-metrics · 7b56eb38
  Peter van 't Hof authored 10 years ago
  
  7b56eb38
- Switched to biopet markduplicates · 349330de
  Peter van 't Hof authored 10 years ago
  
  349330de
- Switched to biopet markduplicates · 9add492d
  Peter van 't Hof authored 10 years ago
  
  9add492d
- First version of working bam-metrics pipeline · 97327078
  Peter van 't Hof authored 10 years ago
  
  97327078
- Added default vmem · 801ac09e
  Peter van 't Hof authored 10 years ago
  
  801ac09e
- Disabled command to report for java jobs · 4b5b6c56
  Peter van 't Hof authored 10 years ago
  
  4b5b6c56
- changed version command to def · ddfac817
  Peter van 't Hof authored 10 years ago
  
  ddfac817
- changed version command to def · c340b559
  Peter van 't Hof authored 10 years ago
  
  c340b559
- Added BiopetFlagstat · 07c486e9
  Peter van 't Hof authored 10 years ago
  
  07c486e9
- Added script for bed to picard interval file · cfe60c25
  Peter van 't Hof authored 10 years ago
  
  cfe60c25
- Added samtools flagstat · 83b6e834
  Peter van 't Hof authored 10 years ago
  
  83b6e834
- Added some picard tools to biopet · fcaea52d
  Peter van 't Hof authored 10 years ago
  
  fcaea52d