Long-read Tumor–Normal SV Pipeline (LOng read Variant ExploreR, SVLover)

A Nextflow pipeline for tumor–normal long-read whole-genome sequencing (WGS) analysis using PacBio HiFi data.
The workflow performs mapping, germline variant calling, haplotype phasing, somatic structural variant (SV) detection with multiple callers, and SV merging.

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Workflow Overview

1. Mapping & QC
   minimap2, samtools, pandepth

2. Germline SV Calling
   pbsv

3. Germline SNV Calling
   DeepVariant (PACBIO model)

4. Phasing & Haplotagging
   HiPhase

5. Somatic SV Calling

   • nanomonsv
   • Severus
   • SAVANA
   • SVision-Pro

6. SV Merging
   SURVIVOR (SVs supported by ≥2 callers)

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Inputs

• Tumor HiFi BAM
• Normal HiFi BAM
• Reference genome (T2T-CHM13)
• minimap2 index
• Tandem repeat annotation (for pbsv / Severus)

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Outputs

• Phased tumor and normal BAM files
• Germline SNV and SV VCFs
• Somatic SV VCFs from individual callers
• Merged somatic SV VCF (merged.2caller.vcf)

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Usage

nextflow run main.nf \
  --normalinput normal.bam \
  --tumorinput tumor.bam \
  --reference chm13v2.0.fa \
  --index minimap2_index