Overview
Overview of the constituting components
GatherSampleEvidence
Gather Sample Evidence
EvidenceQC
Evidence QC
StripyWorkflow
STRipy repeat-expansion calling
TrainGCNV
Train gCNV
GatherBatchEvidence
Gather Batch Evidence
ClusterBatch
Cluster Batch
GenerateBatchMetrics
Generate Batch Metrics
FilterBatch
Filter Batch
MergeBatchSites
Merge Batch Sites
GenotypeBatch
Genotype Batch
RegenotypeCNVs
Regenotype CNVs
CombineBatches
Cross-batch variant clustering
ResolveComplexVariants
Complex SV discovery
GenotypeComplexVariants
Complex SV genotyping
CleanVcf
VCF cleaning
RefineComplexVariants
Refines and filters complex variants
JoinRawCalls
Clusters unfiltered variants across batches
SVConcordance
Annotates concordance with raw calls
ScoreGenotypes
Scores genotypes to optimize GQ recalibrator model
FilterGenotypes
Filters genotypes using GQ recalibrator model
AnnotateVcf
Annotate VCF
MainVcfQC
VCF QC plotting
VisualizeCnvs
Visualize CNVs