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NGS_DNA-3.2.2 pipeline (Caribou)
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@RoanKanninga RoanKanninga released this 16 Apr 21:30
· 674 commits to master since this release
3.2.2
1c87727
  • Changed CoveragePerBase protocol into CoverageCalculations
  • Added Coverage calculations for subset bed files (LEVER, NEURO, SSID and GEO)
  • Changed output for coverage per target and coverage per base
  • CoveragePerBase added missing make genesOnly file + VariantCalling bug (double brackets)
  • increased memory for MarkDuplicates
  • improved the copy prmtotmp data (when prm is not available on zinc-finger it will download it from calculon)
  • bugfix in CheckIlluminaEncoding (where '++' is not used anymore, it is now '+1')
  • added automating:
    • start of pipeline
    • copying to prm
    • copying to zinc-finger
  • fixed the duplication rate in the QC report
  • Made new QCReport (in html)
  • bugfix #439 fixing the GenderCalculate
  • bugfix #457 fixing CheckIlluminaEncoding
  • bugfix #463
  • fix issue with samples on multiple lanes and counting number of samples in generate.sh
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