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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 5 main steps:

Preprocessing:

  • MapReads - Map reads with BWA
  • MergeBams - Merge BAMs if multilane samples
  • MarkDuplicates - Mark Duplicates with GATK4
  • CreateRecalibrationTable - Create Recalibration Table with BaseRecalibrator
  • RecalibrateBam - Recalibrate Bam with PrintReads

Germline Variant Calling:

  • CreateIntervalBeds - Create and sort intervals into bed files
  • RunHaplotypecaller - Run HaplotypeCaller for Germline Variant Calling (Parallelized processes)
  • RunGenotypeGVCFs - Run HaplotypeCaller for Germline Variant Calling (Parallelized processes)
  • ConcatVCF - Merge results from paralellized callers
  • RunSingleStrelka - Run Strelka for Germline Variant Calling
  • RunSingleManta - Run Manta for Single Structural Variant Calling

Somatic Variant Calling:

  • CreateIntervalBeds - Create and sort intervals into bed files
  • RunMutect2 - Run MuTect2 for Variant Calling (Parallelized processes)
  • RunFreeBayes - Run FreeBayes for Variant Calling (Parallelized processes)
  • ConcatVCF - Merge results from paralellized variant callers
  • RunStrelka - Run Strelka for Variant Calling
  • RunStrelkaBP - Run Strelka Best Practices for Variant Calling
  • RunManta - Run Manta for Structural Variant Calling
  • RunSingleManta - Run Manta for Single Structural Variant Calling
  • RunAlleleCount - Run AlleleCount to prepare for ASCAT
  • RunConvertAlleleCounts - Run convertAlleleCounts to prepare for ASCAT
  • RunAscat - Run ASCAT for CNV

Report and QC:

  • RunFastQC - Run FastQC for QC on fastq files
  • RunSamtoolsStats - Run Samtools stats on recalibrated BAM files
  • RunBamQC - Run qualimap BamQC on recalibrated BAM files
  • RunBcftoolsStats - Run BCFTools stats on vcf files
  • RunVcftools - Run VCFTools on vcf files
  • GetVersionAlleleCount - Get version of tools
  • GetVersionASCAT - Get version of tools
  • GetVersionSnpeff - Get version of tools
  • GetVersionVEP - Get version of tools
  • GetVersionAll - Get version of tools
  • RunMultiQC - Run MultiQC on reports

Annotation:

  • RunSnpeff - Run snpEff for annotation of vcf files
  • RunVEP - Run VEP for annotation of vcf files
  • CompressVCF - Compress and index vcf files using tabix