purple

performs purity and ploidy estimation

Overview

Dependencies

PURPLE

Usage

Cromwell

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

Inputs

Required workflow parameters:

Parameter	Value	Description
`tumour_bam`	File	Input tumor file (bam)
`tumour_bai`	File	Input tumor file index (bai)
`normal_bam`	File	Input normal file (bam)
`normal_bai`	File	Input normal file index (bai)
`normal_name`	String	Name of normal sample
`tumour_name`	String	Name of tumour sample

Optional workflow parameters:

Parameter	Value	Default	Description
`genomeVersion`	String	"38"	Genome Version, only 38 supported
`doSV`	Boolean	true	include somatic structural variant calls, true/false
`doSMALL`	Boolean	true	include somatic small (SNV+indel) calls, true/false

Optional task parameters:

Parameter	Value	Default	Description
`amber.amberScript`	String	"java -Xmx32G -cp $HMFTOOLS_ROOT/amber.jar com.hartwig.hmftools.amber.AmberApplication"	location of AMBER script
`amber.threads`	Int	8	Requested CPU threads
`amber.memory`	Int	32	Memory allocated for this job (GB)
`amber.timeout`	Int	100	Hours before task timeout
`cobalt.colbaltScript`	String	"java -Xmx8G -cp $HMFTOOLS_ROOT/cobalt.jar com.hartwig.hmftools.cobalt.CobaltApplication"	location of COBALT script
`cobalt.gamma`	String	100	gamma (penalty) value for segmenting
`cobalt.threads`	Int	8	Requested CPU threads
`cobalt.memory`	Int	32	Memory allocated for this job (GB)
`cobalt.timeout`	Int	100	Hours before task timeout
`filterSV.vcf`	File?	None	VCF file for filtering
`filterSV.gripssScript`	String	"java -Xmx80G -jar $HMFTOOLS_ROOT/gripss.jar"	location and java call for gripss jar
`filterSV.hard_min_tumor_qual`	Int	500	Any variant with QUAL less than x is filtered
`filterSV.filter_sgls`	String	"-filter_sgls"	include filtering of single breakends
`filterSV.memory`	Int	80	Memory allocated for this job (GB)
`filterSV.threads`	Int	1	Requested CPU threads
`filterSV.timeout`	Int	100	Hours before task timeout
`filterSMALL.vcf`	File?	None	VCF file for filtering
`filterSMALL.vcf_index`	File?	None	index of VCF file for filtering
`filterSMALL.bcftoolsScript`	String	"$BCFTOOLS_ROOT/bin/bcftools"	location for bcftools
`filterSMALL.genome`	String	"$HG38_ROOT/hg38_random.fa"	reference fasta
`filterSMALL.regions`	String	"chr1,chr10,chr11,chr12,chr13,chr14,chr15,chr16,chr17,chr18,chr19,chr2,chr20,chr21,chr22,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chrX,chrY"	regions/chromosomes to include
`filterSMALL.difficultRegions`	String	"--targets-file $HG38_DAC_EXCLUSION_ROOT/hg38-dac-exclusion.v2.bed"	regions to exclude because they are difficult
`filterSMALL.tumorVAF`	String	"0.001"	minimum variant allele frequency for tumour calls to pass filter
`filterSMALL.modules`	String	"bcftools/1.9 hg38/p12 hg38-dac-exclusion/1.0"	Required environment modules
`filterSMALL.threads`	Int	8	Requested CPU threads
`filterSMALL.memory`	Int	32	Memory allocated for this job (GB)
`filterSMALL.timeout`	Int	100	Hours before task timeout
`runPURPLE.purpleScript`	String	"java -Xmx8G -jar $HMFTOOLS_ROOT/purple.jar"	location of PURPLE script
`runPURPLE.threads`	Int	8	Requested CPU threads
`runPURPLE.memory`	Int	32	Memory allocated for this job (GB)
`runPURPLE.timeout`	Int	100	Hours before task timeout
`LINX.linxScript`	String	"java -Xmx32G -cp $HMFTOOLS_ROOT/linx.jar com.hartwig.hmftools.linx.LinxApplication"	location of LINX script
`LINX.threads`	Int	8	Requested CPU threads
`LINX.memory`	Int	32	Memory allocated for this job (GB)
`LINX.timeout`	Int	100	Hours before task timeout

Outputs

Output	Type	Description
`purple_qc`	File	QC results from PURPLE
`purple_purity`	File	tab seperated Purity estimate from PURPLE
`purple_purity_range`	File	tab seperated range of Purity estimate from PURPLE
`purple_segments`	File	tab seperated segments estimated by PURPLE
`purple_cnv`	File	tab seperated somatic copy number variants from PURPLE
`purple_cnv_gene`	File	tab seperated somatic gene-level copy number variants from PURPLE
`purple_SV_index`	File?	Structural Variant .vcf index edited by PURPLE
`purple_SV`	File?	Structural Variant .vcf edited by PURPLE
`purple_SMALL_index`	File?	SNV+IN/DEL .vcf index edited by PURPLE
`purple_SMALL`	File?	SNV+IN/DEL .vcf edited by PURPLE

Commands

This section lists commands run by the PURPLE workflow

Run AMBER

 ~{amberScript} \
   -reference ~{normal_name} -reference_bam ~{normal_bam} \
   -tumor ~{tumour_name} -tumor_bam ~{tumour_bam} \
   -output_dir ~{tumour_name}.amber/ \
   -loci ~{PON} \
   -ref_genome_version ~{genomeVersion}

Run COBALT

 ~{colbaltScript} \
   -reference ~{normal_name} -reference_bam ~{normal_bam} \
   -tumor ~{tumour_name} -tumor_bam ~{tumour_bam} \
   -output_dir ~{tumour_name}.cobalt/ \
   -gc_profile ~{gcProfile} \
   -pcf_gamma ~{gamma}

Filter structural variant VCFs using GRIPSS, this is optional but recommended

 ~{gripssScript} \
     -vcf ~{vcf}  \
     -sample ~{tumour_name} -reference ~{normal_name} \
     -ref_genome_version ~{genomeVersion} \
     -ref_genome ~{refFasta} \
     -pon_sgl_file ~{pon_sgl_file} \
     -pon_sv_file ~{pon_sv_file} \
     -known_hotspot_file ~{known_hotspot_file} \
     -repeat_mask_file ~{repeat_mask_file} \
     -output_dir gripss/ \
     -hard_min_tumor_qual ~{hard_min_tumor_qual} \
     ~{filter_sgls}

Filter small variant (SNV + in/del) VCFs using bcftools, this is optional but recommended

  ~{bcftoolsScript} view -f "PASS" -S samples.txt -r ~{regions} ~{difficultRegions} ~{vcf} |\
  ~{bcftoolsScript} norm --multiallelics - --fasta-ref ~{genome} |\
  ~{bcftoolsScript} filter -i "(FORMAT/AD[0:1])/(FORMAT/AD[0:0]+FORMAT/AD[0:1]) >= ~{tumorVAF}"  > ~{tumour_name}.PASS.vcf

Run PURPLE

 ~{purpleScript} \
   -ref_genome_version ~{genomeVersion} \
   -ref_genome ~{refFasta}  \
   -gc_profile ~{gcProfile} \
   -ensembl_data_dir ~{ensemblDir}  \
   -reference ~{normal_name} -tumor ~{tumour_name}  \
   -amber ~{tumour_name}.amber -cobalt ~{tumour_name}.cobalt \
   ~{"-somatic_sv_vcf " + SV_vcf} \
   ~{"-somatic_vcf " + smalls_vcf} \
   -output_dir ~{tumour_name}.purple \
   -no_charts

Run LINX, if structural variant calls from GRIDSS are included

 ~{linxScript} \
   -sample ~{tumour_name} \
   -ref_genome_version ~{genomeVersion} \
   -ensembl_data_dir ~{ensemblDir}  \
   -check_fusions \
   -known_fusion_file ~{fusions_file} \
   -purple_dir ~{tumour_name}.purple \
   -output_dir ~{tumour_name}.linx

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/purple