Skip to content

PacBio Twist Cancer Panel

Workflow Overview

The following simplified workflow diagram shows the main data flow in the PacBio Twist Cancer panel analysis:

Fada Simplified Workflow

Figure: Simplified workflow showing the main data flow from raw PacBio data through alignment (pbmm2) to variant calling tools and quality control metrics.

Complete Pipeline Rulegraph

For the complete view of all rules and dependencies:

Pacbio Twist Cancer Rulegraph

Figure: Complete workflow showing all dependencies between rules in the fada pipeline for PacBio Twist cancer workflow. Each node represents a rule, with arrows indicating data flow and dependencies.

Output Files

This document describes the output files generated by the PacBio Twist Cancer panel workflow. All results are organized under results/{sample}/ with the following directory structure:

results/
├── {sample}/
│   ├── {sample}_coverage_report.xlsx  # excel coverage report
│   ├── cram/                          # Alignment file
│   ├── snv_indels/                    # Small variant calls
│   ├── cnv_sv/                        # Copy number and structural variants
│   └── paraphase/                     # Paralog-specific variant analysis
├── multiqc_pacbio_twist_cancer.html   # Quality control report

Alignment Files (CRAM)

Compressed Alignment Files

  • File: results/{sample}/cram/{sample}.cram

  • Description: Compressed alignment file containing mapped reads in CRAM format

  • File: results/{sample}/cram/{sample}.cram.crai

  • Description: Index file for the CRAM file

Small Variant Files (SNVs & Indels)

Hard-Filtered Variants

  • File: results/{sample}/snv_indels/{sample}.hard-filtered.vcf.gz
  • Description: Phased SNVs and indels in VCF

  • Filter: PASS variants only

  • File: results/{sample}/snv_indels/{sample}.hard-filtered.vcf.gz.tbi

  • Description: Tabix index for the hard-filtered VCF

Soft-Filtered Variants (with Phasing)

  • File: results/{sample}/snv_indels/{sample}.deepvariant.soft-filtered.vcf.gz

  • Description: Phased DeepVariant SNV and INDEL calls, includes RefCalls

  • File: results/{sample}/snv_indels/{sample}.deepvariant.soft-filtered.vcf.gz.tbi

  • Description: Tabix index for the soft-filtered VCF

Copy Number Variants & Structural Variants

Merged CNV/SV Calls

  • File: results/{sample}/cnv_sv/{sample}.cnv_sv.vcf.gz
  • Description: Combined CNV and SV calls from Sawfish and CNVkit (SVDB merged)

  • Callers: Integrated results from CNVkit, Sawfish, and Sniffles2

  • File: results/{sample}/cnv_sv/{sample}.cnv_sv.vcf.gz.tbi

  • Description: Tabix index for the merged CNV/SV VCF

CNVkit Results

  • File: results/{sample}/cnv_sv/{sample}.cnvkit.vcf.gz

  • Description: Large Copy number variants called by CNVkit with gene annotations

  • File: results/{sample}/cnv_sv/{sample}.cnvkit.vcf.gz.tbi

  • Description: Tabix index for the CNVkit VCF

  • File: results/{sample}/cnv_sv/{sample}.cnv_report.html

  • Description: Interactive HTML report showing CNV analysis results

Sawfish Results

  • File: results/{sample}/cnv_sv/{sample}.sawfish.vcf.gz

  • Description: Structural variants called by Sawfish

  • File: results/{sample}/cnv_sv/{sample}.sawfish.vcf.gz.tbi

  • Description: Tabix index for the Sawfish VCF

Sniffles2 Results

  • File: results/{sample}/cnv_sv/{sample}.sniffles2.vcf.gz

  • Description: Structural variants called by Sniffles2

  • File: results/{sample}/cnv_sv/{sample}.sniffles2.vcf.gz.tbi

  • Description: Tabix index for the Sniffles2 VCF

Sniffles2 Mosaic Variants

  • File: results/{sample}/cnv_sv/{sample}.sniffles2.mosaic.vcf.gz

  • Description: Low-frequency mosaic structural variants detected by Sniffles2

  • File: results/{sample}/cnv_sv/{sample}.sniffles2.mosaic.vcf.gz.tbi

  • Description: Tabix index for the mosaic Sniffles2 VCF

Paraphase Analysis (Paralog-Specific Variants)

Alignment Files

  • File: results/{sample}/paraphase/{sample}.paraphase.bam

  • Description: Paraphase-processed alignment file with paralog assignment

  • File: results/{sample}/paraphase/{sample}.paraphase.bam.bai

  • Description: Index file for the Paraphase BAM

Analysis Results

  • File: results/{sample}/paraphase/{sample}.paraphase.json
  • Description: Detailed Paraphase analysis results in JSON format

Gene-Specific VCFs

  • File: results/{sample}/paraphase/{sample}.paraphase.{gene}.vcf.gz
  • Description: Paralog-specific variant calls for individual genes

  • Genes:

  • pms2

  • File: results/{sample}/paraphase/{sample}.paraphase.{gene}.vcf.gz.tbi

  • Description: Tabix index for gene-specific Paraphase VCFs

Quality Control & Reports

MultiQC Report

  • File: results/multiqc_pacbio_twist_cancer.html
  • Description: Comprehensive quality control report aggregating metrics across all samples
  • Content:
  • Read quality metrics
  • Alignment statistics
  • Coverage analysis
  • Variant calling metrics
  • Sample comparison plots

Coverage Report

  • File: results/{sample}/{sample}_coverage_report.xlsx
  • Description: Detailed coverage analysis report in Excel format
  • Use: Per-sample coverage assessment for clinical reporting
  • Content:
  • Target region coverage statistics
  • Per-gene coverage metrics
  • PGRS coverage analysis
  • Exon-level coverage details