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NGS_DNA-3.2.1 pipeline (Caribou)
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@RoanKanninga RoanKanninga released this 22 Dec 14:49
· 986 commits to master since this release
3.2.1
dcb4894 
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Major changes:

  • Replaced Picard tools SortBam, MergeBam and MarkDuplicates for Sambamba tools
  • renamed CheckSex protocol to GenderCheck
  • Splitted the metrics calculations
  • added CramConversion (turned off in workflow)
  • added CoveragePerTarget
  • updated to new compute version v15.12.4
  • upgraded to Java 8

Minor changes + bugfixes

  • fixed GenderCheck for a WGS sample
  • extended walltime for Delly and added more memory
  • changed PERCENTAGE_DUPLICATES to PERCENT_DUPLICATION in dedup metrics (QC report)
  • added new batch options (per chr or 1 batch)
  • added #string project to every protocol
  • fixed VariantCalling bug (sex is Unknown bug)
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