📄️ Overview
Overview of the constituting components
📄️ GatherSampleEvidence
Gather Sample Evidence
📄️ EvidenceQC
Evidence QC
📄️ 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