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Task (.wdl), Run (.wdl) - Coggle Diagram
Task (.wdl)
SNV/INDEL
VarDict (call)
VarDict (teststrandbias)
Vardict (var2vcf)
VCFtools (Sort)
VT (Decompose)
VT (Normalization)
GATK (SelectVariants)
VCFanno
VCF Filter
set target
GATK4 (cleansam)
GATK4 (Mutect2)
GATK4 (GetPileupSummary)
GATK4 (Calculate contamination)
GATK4 (FilterMutectcall)
GATK4
(CollectSequencingArtifactMetrics)
GATK4 (FilterByOrientationBias)
DUP/DEL/INV filter
VCF Merge
Ensembl Annotation (vep)
Ensembl Filter (converter)
Population DB Annotation
Alignment
BWA (aln)
Input
Command
Output
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BWA (sampe)
Input
Command
Output
Picard (MarkDuplicates)
Input
Command
Output
GATK (IndelRealigner)
Input
Command
Output
BaseRecalibration
GATK (CountCovariates)
Input
Command
Output
GATK (TableRecalibration)
Input
Command
Output
Picard (SortSam)
Input
Command
Output
Interpretation
PCGR
SNV to Json
Set HGVs nomenclature
Add PCGR evidence to Json (SNV)
CNV to Json
Add PCGR evidence to Json(CNV)
CNV
CNVkit (batch)
CNVkit (call)
Filter CNV
SV
set config
Breakmer
Filter SV
Statistics
FastQC
Command
Output
Input
Run (.wdl)
SNV/INDEL
Normal
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HRD
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whitelist
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Mutect2
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Merge
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Variant Annotation
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SV
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Alignment
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CNV
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Statistics
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