3.3.0 (Hummingbird)

New features

• XHMM
• Convading
• Made script that will generate XHMM and Convading controlsDir
• Gavin (running CADD locally)
• added genderCheck.sh 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

Updates:

• 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

Minor

• 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)