Commits · 9bfb488097603732d28e77e0fbe68596b9d3109f · Mirrors / biopet.biopet

27 Feb, 2015 3 commits
- Added summary to VcfStats · 9bfb4880
  Peter van 't Hof authored Feb 27, 2015
  
  9bfb4880
- Added gvcf mode · 5c545796
  Peter van 't Hof authored Feb 27, 2015
  
  5c545796
- Fix combine variants · f6841e2c
  Peter van 't Hof authored Feb 27, 2015
  
  f6841e2c
26 Feb, 2015 30 commits
- Fix output bam files of mapping · 77d06f6e
  Peter van 't Hof authored Feb 26, 2015
  
  77d06f6e
- Updated Executable · 73995acb
  Peter van 't Hof authored Feb 26, 2015
  
  73995acb
- Merge branch 'develop' into feature-shiva · 51f729f1
  Peter van 't Hof authored Feb 26, 2015
  
  51f729f1
- Added allele modes · 85554525
  Peter van 't Hof authored Feb 26, 2015
  
  85554525
- Adding UnifiedGenotyper · 25ee758d
  Peter van 't Hof authored Feb 26, 2015
  
  25ee758d
- Add gatk variantcalling with haplotypecaller · 3c2bd820
  Peter van 't Hof authored Feb 26, 2015
  
  3c2bd820
- Add variantcalling to summary · 05273365
  Peter van 't Hof authored Feb 26, 2015
  
  05273365
- fix format · 5d9d3661
  Peter van 't Hof authored Feb 26, 2015
  
  5d9d3661
- Added name prefixes · bedfafee
  Peter van 't Hof authored Feb 26, 2015
  
  bedfafee
- Added variantcalling · 9fe575e8
  Peter van 't Hof authored Feb 26, 2015
  
  9fe575e8
- Fix multiple bugs · d6d834e6
  Peter van 't Hof authored Feb 26, 2015
  
  d6d834e6
- fix args · 7f15bd0b
  Peter van 't Hof authored Feb 26, 2015
  
  7f15bd0b
- Add CombineVariants · 4cde9723
  Peter van 't Hof authored Feb 26, 2015
  
  4cde9723
- Add more options · e4c45c85
  Peter van 't Hof authored Feb 26, 2015
  
  e4c45c85
- Added implicit List[File] · 285e2e4d
  Peter van 't Hof authored Feb 26, 2015
  
  285e2e4d
- General gatk · dbccba19
  Peter van 't Hof authored Feb 26, 2015
  
  dbccba19
- Moved to new package · 7c5cd789
  Peter van 't Hof authored Feb 26, 2015
  
  7c5cd789
- Merge branch 'patch-summary' into 'develop' · 42472f08
  bow authored Feb 26, 2015
```
Patch summary

See merge request !108
```
  42472f08
- Fix add jobs to summary · 6cadcab7
  Peter van 't Hof authored Feb 26, 2015
  
  6cadcab7
- Add ShivaVariantcalling · c3a72a11
  Peter van 't Hof authored Feb 26, 2015
  
  c3a72a11
- Add automatic sample detection · bde80bda
  Peter van 't Hof authored Feb 26, 2015
  
  bde80bda
- Fix format · 6362081c
  Peter van 't Hof authored Feb 26, 2015
  
  6362081c
- Added IndelRealigner and BaseRecalibration · 4c2d0bf5
  Peter van 't Hof authored Feb 26, 2015
  
  4c2d0bf5
- Remove unused imports · 5aae754e
  Peter van 't Hof authored Feb 26, 2015
  
  5aae754e
- Add ShiveGatk · 0d7fce54
  Peter van 't Hof authored Feb 26, 2015
  
  0d7fce54
- Move Shiva to a trait · 492b1223
  Peter van 't Hof authored Feb 26, 2015
  
  492b1223
- Added placeholder for addAll · 3e121e52
  Peter van 't Hof authored Feb 26, 2015
  
  3e121e52
- Complete preproces steps · 33bdaede
  Peter van 't Hof authored Feb 26, 2015
  
  33bdaede
- Fix argument · bebbbbc8
  Peter van 't Hof authored Feb 26, 2015
  
  bebbbbc8
- Added shiva to executable · 245b8b8f
  Peter van 't Hof authored Feb 26, 2015
  
  245b8b8f
24 Feb, 2015 7 commits
- First commit for Shiva · 8af044c7
  Peter van 't Hof authored Feb 24, 2015
  
  8af044c7
- Merge branch 'patch-macs2-callpeaks' into 'develop' · 75029e8e
  bow authored Feb 24, 2015
```
Patch macs2 callpeaks

Patch to fix the argument parsing of modelfold in macs2 callpeak. Test succeeded.

See merge request !105
```
  75029e8e
- Merge branch 'patch-summary_md5' into 'develop' · 5904845a
  bow authored Feb 24, 2015
```
Patch summary md5

Fix on md5 in summary

See merge request !107
```
  5904845a
- Fix to redirect md5 to be write in the ouput dir · 359dcab8
  Peter van 't Hof authored Feb 24, 2015
  
  359dcab8
- Fix to redirect md5 to be write in the ouput dir · e3ed0640
  Peter van 't Hof authored Feb 24, 2015
  
  e3ed0640
- Merge branch 'patch-bowtie' into 'develop' · 85b9861f
  bow authored Feb 24, 2015
```
Patch bowtie

Fix error on paired end reads for bowtie

See merge request !106
```
  85b9861f
- Fix imports · fd8d9ae0
  Peter van 't Hof authored Feb 24, 2015
  
  fd8d9ae0