Contents

1 CNVWorkflow folder structure

CNVworkflow
├── input
│   ├── references
│   ├── bed
├── mutect_output
│   ├── normal_panel
│   └── stat_tumor_only
│   └── normals.merged.min5.vcf
└── purecn_output
    ├── Dx
    │   ├── callableLoci
    │   └── tumor_only_cds
    ├── normal_cov
    ├── normalDB
    ├── PureCN
    │   └── tumor_only
    └── tumor_cov

2 Run PureCN

echo INPUT="/path/to/CNVworkflow/input"
echo MUTECT_OUT="/path/to/CNVworkflow/mutect_output"
echo PCN_OUT="/path/to/CNVworkflow/purecn_output"

Rscript $PURECN/PureCN.R \
    --out $PCN_OUT/PureCN/tumor_only/$SAMPLEID \
    --tumor $PCN_OUT/tumor_cov/${SAMPLEID}_coverage_loess.txt \
    --SAMPLEID ${SAMPLEID} \
    --vcf $MUTECT_OUT/stat_tumor_only/${SAMPLEID}_mutect.vcf \
    --statsfile $MUTECT_OUT/stat_tumor_only/${SAMPLEID}_mutect_stats.txt \
    --normaldb $PCN_OUT/normalDB/normalDB_hg38.rds \
    --normal_panel $PCN_OUT/normalDB/mapping_bias_hg38.rds \
    --intervals $INPUT/bed/baits_hg38_intervals.txt \
    --intervalweightfile $PCN_OUT/normalDB/interval_weights_hg38.txt \
    --snpblacklist hg38_simpleRepeats.bed \
    --genome hg38 \
    --force --postoptimize --seed 123