Several processes are run within the workflow. We divide them for the moment into 5 main steps:
- MapReads - Map reads with BWA
- MergeBams - Merge BAMs if multilane samples
- MarkDuplicates - Mark Duplicates with Picard
- RealignerTargetCreator - Create realignment target intervals
- IndelRealigner - Realign BAMs as T/N pair
- CreateRecalibrationTable - Create Recalibration Table with BaseRecalibrator
- RecalibrateBam - Recalibrate Bam with PrintReads
- 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 HaplotypeCaller
- RunSingleStrelka - Run Strelka for Germline Variant Calling
- RunSingleManta - Run Manta for Single Structural Variant Calling
- CreateIntervalBeds - Create and sort intervals into bed files
- RunMutect1 - Run MuTect1 for Variant Calling (Parallelized processes)
- RunMutect2 - Run MuTect2 for Variant Calling (Parallelized processes)
- RunFreeBayes - Run FreeBayes for Variant Calling (Parallelized processes)
- ConcatVCF - Merge results from Freebayes, MuTect1 and MuTect2
- RunStrelka - Run Strelka 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
- 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
- RunSnpeff - Run snpEff for annotation of vcf files
- RunVEP - Run VEP for annotation of vcf files
