mrdetect

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

Overview

Dependencies

Usage

Cromwell

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

Inputs

Required workflow parameters:

Parameter	Value	Description
`plasmabam`	File	plasma input .bam file
`plasmabai`	File	plasma input .bai file
`outputFileNamePrefix`	String	Prefix for output file
`tumorSampleName`	String	ID for WGS tumor sample, must match .vcf header
`tumorvcf`	File	tumor vcf file, bgzip
`tumorvcfindex`	File	tumor vcf index file

Optional workflow parameters:

Parameter	Value	Default	Description
`controlFileList`	String	"/.mounts/labs/gsi/src/pwgs_hbc/1.0/HBC.bam.list"	tab seperated list of bam and bai files for healthy blood controls

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.genome`	String	"$HG38_ROOT/hg38_random.fa"	Path to loaded genome .fa
`filterVCF.difficultRegions`	String	"--regions-file $HG38_DAC_EXCLUSION_ROOT/hg38-dac-exclusion.v2.bed"	Path to .bed excluding difficult regions, string must include the flag --regions-file
`filterVCF.modules`	String	"bcftools/1.9 hg38/p12 hg38-dac-exclusion/1.0"	Required environment modules
`filterVCF.jobMemory`	Int	64	Memory allocated for this job (GB)
`filterVCF.threads`	Int	4	Requested CPU threads
`filterVCF.timeout`	Int	10	Hours before task timeout
`parseControls.jobMemory`	Int	4	Memory for this task in GB
`parseControls.timeout`	Int	12	Timeout in hours, needed to override imposed limits
`detectControl.plasmaSampleName`	String	basename(plasmabam,".bam")	name for plasma sample (from bam)
`detectControl.tumorSampleName`	String	basename(tumorvcf,".vcf")	name for tumour sample (from vcf)
`detectControl.modules`	String	"mrdetect/1.1.1 pwgs-blocklist/hg38.1"	Required environment modules
`detectControl.jobMemory`	Int	64	Memory allocated for this job (GB)
`detectControl.threads`	Int	4	Requested CPU threads
`detectControl.timeout`	Int	20	Hours before task timeout
`detectControl.pickle`	String	"$MRDETECT_ROOT/bin/MRDetectSNV/trained_SVM.pkl"	trained pickle for detecting real tumor reads
`detectControl.blocklist`	String	"$PWGS_BLOCKLIST_ROOT/blocklist.vcf.gz"	list of sites to exclude from analysis, gzipped
`detectControl.pullreadsScript`	String	"$MRDETECT_ROOT/bin/pull_reads"	pull_reads.py executable
`detectControl.qualityscoreScript`	String	"$MRDETECT_ROOT/bin/quality_score"	quality_score.py executable
`detectControl.filterAndDetectScript`	String	"$MRDETECT_ROOT/bin/filterAndDetect"	filterAndDetect.py executable
`detectSample.plasmaSampleName`	String	basename(plasmabam,".bam")	name for plasma sample (from bam)
`detectSample.tumorSampleName`	String	basename(tumorvcf,".vcf")	name for tumour sample (from vcf)
`detectSample.modules`	String	"mrdetect/1.1.1 pwgs-blocklist/hg38.1"	Required environment modules
`detectSample.jobMemory`	Int	64	Memory allocated for this job (GB)
`detectSample.threads`	Int	4	Requested CPU threads
`detectSample.timeout`	Int	20	Hours before task timeout
`detectSample.pickle`	String	"$MRDETECT_ROOT/bin/MRDetectSNV/trained_SVM.pkl"	trained pickle for detecting real tumor reads
`detectSample.blocklist`	String	"$PWGS_BLOCKLIST_ROOT/blocklist.vcf.gz"	list of sites to exclude from analysis, gzipped
`detectSample.pullreadsScript`	String	"$MRDETECT_ROOT/bin/pull_reads"	pull_reads.py executable
`detectSample.qualityscoreScript`	String	"$MRDETECT_ROOT/bin/quality_score"	quality_score.py executable
`detectSample.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
`snvDetectionResult`	File	Result from SNV detection incl sample HBCs
`pWGS_svg`	File	pWGS svg
`snpcount`	File	number of SNPs in vcf after filtering
`snvDetectionVAF`	File?	VAF from SNV detection for sample
`final_call`	File	Final file of mrdetect results

Commands

This section lists commands run by the MRDetect workflow.

filterVCF

Performs vcf Filtering, followed by processing of individual MRDetect calls. Filters include removing difficult regions (optional), splitting multiallelic loci into one allele per line, removing indels, removing loci by quality metrics (set by tumorVCFfilter) and finally removing SNPs by VAF (set by tumorVAF).

	$BCFTOOLS_ROOT/bin/bcftools view -s ~{tumorbasename} ~{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}" >~{tumorbasename}.SNP.vcf

parseControls

This command processes the list of control files as paired bam/bai files and prints them out for detection.

detectSNVs

MRDetect proceed across three steps. This task is run through for the sample and for all the controls.

1- pull_reads takes any reads in the plasma .bam that corresponds to a SNP in the solid-tumour .vcf.

2- quality_score assesses the likelihood that any read is plasma based on the quality score and the trained pickle.

3- filterAndDetect keeps reads with high plasma likehood and removed those for which SNPs are in the blocklist.

	$MRDETECT_ROOT/bin/pull_reads \
		--bam ~{plasmabam} \
		--vcf ~{tumorvcf} \
		--out PLASMA_VS_TUMOR.tsv

	$MRDETECT_ROOT/bin/quality_score \
		--pickle-name ~{pickle} \
		--detections PLASMA_VS_TUMOR.tsv \
		--output_file PLASMA_VS_TUMOR.svm.tsv

	$MRDETECT_ROOT/bin/filterAndDetect \
		--vcfid ~{tumorSampleName} --bamid ~{plasmaSampleName} \
		--svm PLASMA_VS_TUMOR.svm.tsv \
		--vcf ~{tumorvcf} \
		--output ./ \
		--blocklist ~{blocklist} \
		--troubleshoot

snvDetectionSummary

Finally, pwg_test.R will process the controls and the sample to make a final call.

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

	$MRDETECT_ROOT/bin/pwg_test  \
		--sampleName ~{outputFileNamePrefix} \
		--results ~{outputFileNamePrefix}.HBCs.csv \
		--candidateSNVsCountFile ~{snpcount} \
		--vafFile ~{vafFile} \
		--pval ~{pvalue}

Support

For support, please file an issue on the Github project or send an email to gsi@oicr.on.ca .

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oicr-gsi/mrdetect