DRAGEN Heme v1.0
pipeline:
sampleType: DNA
successMarkerFile: "Results/MetricsOutput.tsv"
failureMarkerFile: "./failure.txt"
sampleSheet:
filePath: "SampleSheet.csv"
dataHeaderRowMarker: "[Heme_Data]"
jointFiles:
purityPloidyFiles: "Results/{sampleId.DNA}/{sampleId.DNA}.cnv.vcf.gz, Optional"
snvFiles: "Results/{sampleId.DNA}/{sampleId.DNA}.hard-filtered.vcf.gz"
cnvFiles: "Results/{sampleId.DNA}/{sampleId.DNA}.cnv.vcf.gz, Optional"
svFiles: "Results/{sampleId.DNA}/{sampleId.DNA}.sv.small_indel_dedup.filtered.vcf.gz, Optional"
metricsQCFile: "Results/MetricsOutput.tsv, Optional"
sampleFiles:
tumorPairId:
visualizationFiles:
coverageFiles: "Logs_Intermediates/DragenCaller/{sampleId.DNA}/{sampleId.DNA}.tumor.target.counts.gc-corrected.gz, Optional"
ballelesFiles: "Logs_Intermediates/DragenCaller/{sampleId.DNA}/{sampleId.DNA}.tumor.baf.bedgraph.gz, Optional"
alignmentFiles:
dnaBamFile: "Logs_Intermediates/DragenCaller/{sampleId.DNA}/{sampleId.DNA}_tumor.bam, Optional"
dnaBaiFile: "Logs_Intermediates/DragenCaller/{sampleId.DNA}/{sampleId.DNA}_tumor.bam.bai, Optional"
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