wgsMetrics

Workflow to run picard WGSMetrics

Overview

Dependencies

• picard 2.21.2

Usage

Cromwell

java -jar cromwell.jar run wgsMetrics.wdl --inputs inputs.json

Inputs

Required workflow parameters:

Parameter	Value	Description
inputBam	File	Input file (bam or sam).
reference	String	reference genome of inputs sample

Optional workflow parameters:

Parameter	Value	Default	Description
outputFileNamePrefix	String	basename(inputBam,'.bam')	Output prefix to prefix output file names with.

Optional task parameters:

Parameter	Value	Default	Description
collectWGSmetrics.picardJar	String	"$PICARD_ROOT/picard.jar"	Picard jar file to use
collectWGSmetrics.metricTag	String	"WGS"	metric tag is used as a file extension for output
collectWGSmetrics.filter	String	"LENIENT"	Picard filter to use
collectWGSmetrics.jobMemory	Int	18	memory allocated for Job
collectWGSmetrics.coverageCap	Int	500	Coverage cap, picard parameter
collectWGSmetrics.timeout	Int	24	Maximum amount of time (in hours) the task can run for.

Outputs

Output	Type	Description	Labels
outputWGSMetrics	File	File with collected metrics

Commands

This section lists command(s) run by wgsmetrics workflow

• Running wgsmetrics

A simple wrapper workflow for running picard CollectWgsMetrics.

    java -Xmx[MEMORY]G -jar picard
    CollectWgsMetrics 
    TMP_DIR=picardTmp 
    R=REF_FASTA 
    COVERAGE_CAP=COVERAGE_CAP 
    INPUT=INPUT_BAM 
    OUTPUT=PREFIX.METRICS_TAG.txt" 
    VALIDATION_STRINGENCY=FILTER

Support

For support, please file an issue on the Github project or send an email to [email protected] .

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