Commits · f0b44cf826a4a5757ac182a97a117c249945cfbe · Mirrors / biopet.biopet

06 Oct, 2014 1 commit
- Added ploidy option · f0b44cf8
  Peter van 't Hof authored Oct 06, 2014
  
  f0b44cf8
30 Sep, 2014 1 commit
- Fix genotyping on deleted bases · be5d06cc
  Peter van 't Hof authored Sep 30, 2014
  
  be5d06cc
29 Sep, 2014 5 commits
- Spelling error · 5b7ea34d
  Peter van 't Hof authored Sep 29, 2014
  
  5b7ea34d
- Changed default vmem · a59a1a55
  Peter van 't Hof authored Sep 29, 2014
  
  a59a1a55
- Changed default vmem · 24a1e5b0
  Peter van 't Hof authored Sep 29, 2014
  
  24a1e5b0
- Added framework for new pipeline · 61af28f8
  Peter van 't Hof authored Sep 29, 2014
  
  61af28f8
- allele option is now optional · dfb4c3b2
  Peter van 't Hof authored Sep 29, 2014
  
  dfb4c3b2
26 Sep, 2014 6 commits
- Fix bug on executable · 109d9888
  Peter van 't Hof authored Sep 26, 2014
  
  109d9888
- Removed samtools view · aac2adc8
  Peter van 't Hof authored Sep 26, 2014
  
  aac2adc8
- Added merge and filter · 25fd5d1a
  Peter van 't Hof authored Sep 26, 2014
  
  25fd5d1a
- Added merge · 0f10e443
  Peter van 't Hof authored Sep 26, 2014
  
  0f10e443
- Added Quality and BAQ options · 17e37c17
  Peter van 't Hof authored Sep 26, 2014
  
  17e37c17
- Added filter on HET_REF · aac5ea06
  Peter van 't Hof authored Sep 26, 2014
  
  aac5ea06
22 Sep, 2014 13 commits
- Added genotypes to raw vcf · 20c57725
  Peter van 't Hof authored Sep 22, 2014
  
  20c57725
- Pass filter variants at combine step · 6cae83fa
  Peter van 't Hof authored Sep 22, 2014
  
  6cae83fa
- Fix output dirs · f354bcf0
  Peter van 't Hof authored Sep 22, 2014
  
  f354bcf0
- Added merge step · 297f3c15
  Peter van 't Hof authored Sep 22, 2014
  
  297f3c15
- Fix bug on missing index · 39ee5e10
  Peter van 't Hof authored Sep 22, 2014
  
  39ee5e10
- Fixe namespaces · 693e61b8
  Peter van 't Hof authored Sep 22, 2014
  
  693e61b8
- Run after graph after script · a1f807a5
  Peter van 't Hof authored Sep 22, 2014
  
  a1f807a5
- recalibration is now optional · 52cc9aaf
  Peter van 't Hof authored Sep 22, 2014
  
  52cc9aaf
- Switch to filtered vcf files · 3b8f9b04
  Peter van 't Hof authored Sep 22, 2014
  
  3b8f9b04
- Remove unused lines · 3d936282
  Peter van 't Hof authored Sep 22, 2014
  
  3d936282
- Added filter step · 22b4b757
  Peter van 't Hof authored Sep 22, 2014
  
  22b4b757
- Now outputs a multi allelic vcf file · f0fd2b99
  Peter van 't Hof authored Sep 22, 2014
  
  f0fd2b99
- Fix config name space · 4c3b9198
  Peter van 't Hof authored Sep 22, 2014
  
  4c3b9198
17 Sep, 2014 2 commits
- Added overlap metrics plot · f49a3ad8
  Peter van 't Hof authored Sep 17, 2014
  
  f49a3ad8
- Output files change to gz output · 03325266
  Peter van 't Hof authored Sep 17, 2014
  
  03325266
16 Sep, 2014 1 commit
- Added known option · 168c2d80
  Peter van 't Hof authored Sep 16, 2014
  
  168c2d80
15 Sep, 2014 2 commits
- Fix counting on big files · 5f8092e9
  Peter van 't Hof authored Sep 15, 2014
  
  5f8092e9
- Joint variantcalling is now optional · b36a4b5e
  Peter van 't Hof authored Sep 15, 2014
  
  b36a4b5e
12 Sep, 2014 9 commits
- Changed test files · 73f8e468
  Peter van 't Hof authored Sep 12, 2014
  
  73f8e468
- Added combine multisample variantcalling · c1748449
  Peter van 't Hof authored Sep 12, 2014
  
  c1748449
- Change to sample field · 3eb548bd
  Peter van 't Hof authored Sep 12, 2014
  
  3eb548bd
- Change to biopet gatk modules · fbf778ac
  Peter van 't Hof authored Sep 12, 2014
  
  fbf778ac
- Added CombineVariants · 70b36acd
  Peter van 't Hof authored Sep 12, 2014
  
  70b36acd
- Add output_mode option · 8d17bcbb
  Peter van 't Hof authored Sep 12, 2014
  
  8d17bcbb
- Added joint variantcalling step · a5616824
  Peter van 't Hof authored Sep 12, 2014
  
  a5616824
- Function for gvcf mode · 8820b625
  Peter van 't Hof authored Sep 12, 2014
  
  8820b625
- Changed multisample trait · 7772e165
  Peter van 't Hof authored Sep 12, 2014
  
  7772e165