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Task, Configure, ONCO, ctDNA, Input - Coggle Diagram
Task
BWA (mem)
Command
Output
#
BWA (aln)
Command
Output
#
BWA (sampe)
Command
Output
#
GATK (MarkDuplicates)
Command
Output
#
GATK (TableRecalibration)
Command
Output
#
GATK (CountCovariates)
Command
Output
#
GATK (IndelRealigner)
Command
Output
#
GATK (ApplyBQSR)
Command
Output
#
GATK (BaseRecalibrator)
Command
Output
#
BBDuk
Command
Output
GATK (AddOrReplaceReadGroups)
Command
Output
FastQC
Command
Output
#
#
Mege BAM
Command
Output
#
Filter UHS
Command
Output
Configure
FastQC
BWA (v0.5.9)
BWA (v0.7.10)
BWA (v0.7.17)
GATK (v1.6.5)
GATK (v4.0.6.0)
GATK (v4.1.0.0)
GATK (v4.1.3.0)
Samtools (v1.9)
ONCO
Run FastQC
Input
#
Command
#
Output
Tool
#
Run BWA (aln)
Input
#
Output
Command
#
Tool
#
Run BWA (sampe)
Input
#
Output
Command
#
Tool
#
Run Mark Duplicate
Input
#
Output
Command
#
Tool
#
Run Indel Realign
Input
#
Output
Command
#
Tool
#
Run Count Covariates
Input
#
Output
Command
#
Tool
#
Run Base Recalibration
Input
#
Output
Command
#
Tool
#
ctDNA
Run FastQC
Input
#
Command
#
Output
Tool
#
Run Filter UHS
Input
#
Output (UHS)
Command
Tool
#
Output (Non-UHS)
Run Apply BQSR
Input
#
Output
Command
#
Tool
#
Run BWA (mem)
Input
#
Output
Command
#
Tool
#
Run Mark Duplicate
Input
#
Output
Command
Tool
#
Run Base Recalibration
Input
#
Output
Command
#
Tool
#
Run Merge BAM
Input
#
#
Output
Command
#
Input
Fastq File