mrdetect

Workflow for MRdetect, detection of Minimal Residual Disease from paired tumor-plasma sample

Overview

Dependencies

• mrdetect 1.0
• bcftools 1.9

Usage

Cromwell

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

Inputs

Required workflow parameters:

Parameter	Value	Description
tumorSampleName	String	ID for WGS tumor sample, must match .vcf header
tumorvcf	File	tumor vcf file, bgzip
tumorvcfindex	File	tumor vcf index file
reference	String	genome reference build. Only hg38 supported
instrument	String	sequencing instrument used (Illumina NovaSeq X Plus or Illumina NovaSeq 6000)

Optional workflow parameters:

Parameter	Value	Default	Description
plasmabam	File?	None	plasma input .bam file
plasmabai	File?	None	plasma input .bai file
plasmaSampleName	String?	None	name for plasma sample (from bam)
full_analysis_mode	Boolean	true	Enable full analysis mode with this flag

Optional task parameters:

Parameter	Value	Default	Description
filterVCF.tumorVCFfilter	String	"FILTER~'haplotype'	FILTER~'clustered_events'
filterVCF.tumorVAF	String	"0.1"	Variant Allele Frequency for tumor VCF
filterVCF.jobMemory	Int	64	Memory allocated for this job (GB)
filterVCF.threads	Int	4	Requested CPU threads
filterVCF.timeout	Int	10	Hours before task timeout
parseControls.jobMemory	Int	4	Memory for this task in GB
parseControls.timeout	Int	12	Timeout in hours, needed to override imposed limits
controlPullReads.jobMemory	Int	64	Memory allocated for this job (GB)
controlPullReads.threads	Int	4	Requested CPU threads
controlPullReads.timeout	Int	20	Hours before task timeout
controlPullReads.pullreadsScript	String	"$MRDETECT_ROOT/bin/pull_reads"	pull_reads.py executable
controlQualityScore.jobMemory	Int	64	Memory allocated for this job (GB)
controlQualityScore.threads	Int	4	Requested CPU threads
controlQualityScore.timeout	Int	20	Hours before task timeout
controlQualityScore.pickle	String	"$MRDETECT_ROOT/bin/MRDetectSNV/trained_SVM.pkl"	trained pickle for detecting real tumor reads
controlQualityScore.qualityscoreScript	String	"$MRDETECT_ROOT/bin/quality_score"	quality_score.py executable
controlDetectSNVs.tumorSampleName	String	basename(tumorvcf,".vcf")	name for tumour sample (from vcf)
controlDetectSNVs.jobMemory	Int	64	Memory allocated for this job (GB)
controlDetectSNVs.threads	Int	4	Requested CPU threads
controlDetectSNVs.timeout	Int	20	Hours before task timeout
controlDetectSNVs.blocklist	String	"$PWGS_BLOCKLIST_ROOT/blocklist.vcf.gz"	list of sites to exclude from analysis, gzipped
controlDetectSNVs.filterAndDetectScript	String	"$MRDETECT_ROOT/bin/filterAndDetect"	filterAndDetect.py executable
samplePullReads.jobMemory	Int	64	Memory allocated for this job (GB)
samplePullReads.threads	Int	4	Requested CPU threads
samplePullReads.timeout	Int	20	Hours before task timeout
samplePullReads.pullreadsScript	String	"$MRDETECT_ROOT/bin/pull_reads"	pull_reads.py executable
sampleQualityScore.jobMemory	Int	64	Memory allocated for this job (GB)
sampleQualityScore.threads	Int	4	Requested CPU threads
sampleQualityScore.timeout	Int	20	Hours before task timeout
sampleQualityScore.pickle	String	"$MRDETECT_ROOT/bin/MRDetectSNV/trained_SVM.pkl"	trained pickle for detecting real tumor reads
sampleQualityScore.qualityscoreScript	String	"$MRDETECT_ROOT/bin/quality_score"	quality_score.py executable
sampleDetectSNVs.tumorSampleName	String	basename(tumorvcf,".vcf")	name for tumour sample (from vcf)
sampleDetectSNVs.jobMemory	Int	64	Memory allocated for this job (GB)
sampleDetectSNVs.threads	Int	4	Requested CPU threads
sampleDetectSNVs.timeout	Int	20	Hours before task timeout
sampleDetectSNVs.blocklist	String	"$PWGS_BLOCKLIST_ROOT/blocklist.vcf.gz"	list of sites to exclude from analysis, gzipped
sampleDetectSNVs.filterAndDetectScript	String	"$MRDETECT_ROOT/bin/filterAndDetect"	filterAndDetect.py executable
snvDetectionSummary.pvalue	String	"0.00001"	p-value for HBC error rate
snvDetectionSummary.jobMemory	Int	20	Memory allocated for this job (GB)
snvDetectionSummary.threads	Int	1	Requested CPU threads
snvDetectionSummary.timeout	Int	2	Hours before task timeout
snvDetectionSummary.modules	String	"mrdetect/1.1.1"	Required environment modules
snvDetectionSummary.pwgtestscript	String	"$MRDETECT_ROOT/bin/pwg_test"	executable of pwg_test.R

Outputs

Output	Type	Description	Labels
snvDetectionResult	File?	Result from SNV detection incl sample HBCs	vidarr_label: snvDetectionResult
pWGS_svg	File?	pWGS svg	vidarr_label: pWGS_svg
snpcount	File	number of SNPs in vcf after filtering	vidarr_label: snpcount
snvDetectionVAF	File?	VAF from SNV detection for sample	vidarr_label: snvDetectionVAF
final_call	File?	Final file of mrdetect results	vidarr_label: final_call
filteredvcf	File?	Filtered vcf

Commands

This section lists command(s) run by mrdetect workflow

• Running mrdtect

		set -euo pipefail

		$BCFTOOLS_ROOT/bin/bcftools view -s ~{tumorSampleName} --regions-file ~{difficultRegions} ~{tumorvcf} |\
		$BCFTOOLS_ROOT/bin/bcftools norm --multiallelics - --fasta-ref ~{genome} |\
		$BCFTOOLS_ROOT/bin/bcftools filter -i "TYPE='snps'" |\
		$BCFTOOLS_ROOT/bin/bcftools filter -e "~{tumorVCFfilter}" |\
		$BCFTOOLS_ROOT/bin/bcftools filter -i "(FORMAT/AD[0:1])/(FORMAT/AD[0:0]+FORMAT/AD[0:1]) >= ~{tumorVAF}" > ~{tumorSampleName}.SNP.vcf

		awk '$1 !~ "#" {print}' ~{tumorSampleName}.SNP.vcf | wc -l > ~{tumorSampleName}.SNP.count.txt

		set -euo pipefail

		~{pullreadsScript} \
			--bam ~{plasmabam} \
			--vcf ~{tumorvcf} \
			--out PLASMA_VS_TUMOR.tsv

		set -euo pipefail

		~{qualityscoreScript} \
			--pickle-name ~{pickle} \
			--detections ~{snvDetectionReads} \
			--output_file PLASMA_VS_TUMOR.svm.tsv

		set -euo pipefail

		~{filterAndDetectScript} \
			--vcfid ~{tumorSampleName} --bamid ~{plasmaSampleName} \
			--svm ~{snvDetectionReadsScored} \
			--vcf ~{tumorvcf} \
			--output ./ \
			--blocklist ~{blocklist} 
		mv ~{plasmaSampleName}.mrdetect.results.csv ~{tumorSampleName}_~{plasmaSampleName}.mrdetect.results.csv
		mv ~{plasmaSampleName}.mrdetect.vaf.txt ~{tumorSampleName}_~{plasmaSampleName}.mrdetect.vaf.txt

		python <<CODE
		import os

		with open(os.environ.get("~{controlFileList}")) as f:
			for line in f:
				line = line.rstrip()
				tmp = line.split("\t")
				r = tmp[0] + "\t" + tmp[1]
				print(r)
		f.close()
		CODE

		set -euo pipefail

		cat ~{sep=' ' controlCalls} | awk '$1 !~ "BAM" {print}' > HBCs.csv

		cat ~{sampleCalls} HBCs.csv > ~{plasmaSampleName}.HBCs.csv

		~{pwgtestscript} \
			--sampleName ~{plasmaSampleName} \
			--results ~{plasmaSampleName}.HBCs.csv \
			--candidateSNVsCountFile ~{snpcount} \
			--vafFile ~{vafFile} \
			--pval ~{pvalue} 
		mv ~{plasmaSampleName}.pWGS.svg ~{tumorSampleName}_~{plasmaSampleName}.pWGS.svg
		mv ~{plasmaSampleName}.HBCs.csv ~{tumorSampleName}_~{plasmaSampleName}.HBCs.csv
		mv ~{plasmaSampleName}.mrdetect.txt ~{tumorSampleName}_~{plasmaSampleName}.mrdetect.txt

Support

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

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