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Task (.wdl), Run (.wdl), Configure, Input (ONCO) - Coggle Diagram
Task (.wdl)
SNV/INDEL
VarDict (Somatic)
VarDict (Germline)
VarDict (Strandbias)
VarDict (var2vcf)
VCF Validation
GATK (Mutect2)
GATK (GetPileupSummaries)
GATK (CalculateContamination)
GATK (FilterMutectCalls)
GATK (CollectSequencingArtifactMetrics)
GATK (FilterByOrientationBias)
VCF Merge
Whitelist Filter
Pindel
Alignment
BWA MEM
BWA ALN
GATK (Mark Duplicate)
GATK (Realign)
GATK (Base Recalibration)
GATK (BQSR)
Filter UHS
Merge BAM
BBDuk
FastQC
BWA SAMPE
GATK (CountCovariates)
Statistics
Soft Clip
Remove Secondary Reads (Mark Duplicate)
Remove Secondary Reads (Non-Mark Duplicate)
Samtools Depth (Mark Duplicate)
Samtools Depth (Non-Mark Duplicate)
get MAPQ
Make QC Report
CNV
SV(Fusion)
AMP
ACMG
Run (.wdl)
ONCO (DNA)
Alignment
FastQC
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BWA ALN
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BWA SAMPE
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GATK (Mark Duplicate)
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GATK (Realign)
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GATK (CountCovariates)
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SNV/INDEL
CNV
SV
SOLID (DNA)
BRCA (DNA)
ctDNA (DNA)
SOLID (RNA)
HEME (DNA)
HEME (RNA)
Configure
App
GATK (v4.1.0.0)
GATK (v4.0.6.0)
GATK (v4.1.3.0)
GATK (v1.6.5)
BWA (v0.7.10)
BWA (v0.5.9)
BWA (v0.7.17)
FastQC
Dependencies
Input (ONCO)
Fastq File
Pipeline
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