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3.3.0 (Hummingbird)

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@RoanKanninga RoanKanninga released this 12 Jan 13:25
· 1100 commits to master since this release

New features

  • XHMM
  • Convading
  • Made script that will generate XHMM and Convading controlsDir
  • Gavin (running CADD locally)
  • added to generate script
  • Annotating with SnpEff, CADD, ExAC and GoNL
  • VEP annotation (side step after genotyping (it will not be copied to resultsdir)
  • Manta as main CNV caller (still researchy, diagnostics validation is still not done)
  • copy gVCF WGS samples to prm at the end of the pipeline


  • gender column can now be used by Convading
  • VariantCalling is now outputting in gzip format
  • Compressing variant vcf's in resultsdirectory
  • Optimizing workflow due to parallelisation of certain steps
  • removing windows line breaks automatically in CreateInhouseProjects step
  • Removed VariantCompressing protocol since VariantCalling will automatically compresses its output

Version updates

  • Manta (0.29.5 to 1.0.1)
  • SnpEff (4.1g to 4.3)
  • SnpEff database change from GRCh37.75 to hg19


  • added CoverageCalculations as dependency on countallfinishedfiles
  • CoverageCalculations has now $panel.interval_list instead of $panel.bed
  • removed unused and difficult way of making duplicate statistics
  • Fix in output genderCheck calculation
  • Added Convading and XHMM Controlsdir used in QCReport
  • Automatic detection if data is from a panel or not (Removed diagnostics=diagnostics column check)