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PROCESS.md

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Workflow processes

Several processes are run within the workflow. We divide them for the moment into 3 main steps:

Preprocessing [Stable]:

  • MapReads - Map reads [Stable]
  • MergeBams - Merge BAMs if multilane samples [Stable]
  • MarkDuplicates - Mark Duplicates [Stable]
  • CreateIntervals - Create Intervals [Stable]
  • RealignBams - Realign Bams as T/N pair [Stable]
  • CreateRecalibrationTable - Create Recalibration Table [Stable]
  • RecalibrateBam - Recalibreate Bam [Stable]

Variant Calling:

  • RunHaplotypecaller - Run HaplotypeCaller for GermLine Variant Calling (Parrallelized processes) [Stable]
  • RunMutect1 - Run MuTect1 for Variant Calling (Parrallelized processes) [Stable]
  • RunMutect2 - Run MuTect2 for Variant Calling (Parrallelized processes) [Working]
  • RunFreeBayes - Run FreeBayes for Variant Calling (Parrallelized processes) [Working]
  • RunVardict - Run VarDict for Variant Calling (Parrallelized processes) [Working]
  • ConcatVCF - Merge results from HaplotypeCaller, MuTect1, MuTect2 and VarDict parrallelized processes [Stable]
  • RunStrelka - Run Strelka for Variant Calling [Stable]
  • RunManta - Run Manta for Structural Variant Calling [Need more tests]
  • RunAlleleCount - Run AlleleCount to prepare for Ascat [Stable]
  • RunConvertAlleleCounts - Run convertAlleleCounts to prepare for Ascat [Stable]
  • RunAscat - Run Ascat for CNV [Stable]

Report and QC:

  • RunFastQC - Run FastQC for QC on fastq files [Stable]
  • RunMultiQC - Run MultiQC for report and QC [Stable]