PanelCNV_pipeline

Overview

This pipeline is designed for Target Panel Sequencing (TPS) data analysis. It includes:

• Preprocessing: FastQC, TrimGalore, BWA, Samtools, Picard.
• Base Quality Score Recalibration (BQSR): GATK.
• Variant Calling: GATK, bcftools.
• Copy Number Variation (CNV) Analysis: CNVkit, Control-FREEC.
• Annotation: ANNOTSV.
• Visualization: MultiQC, Event by Chr.

🔧 Features in Design

• Additional annotation enhancements.
• Improved visualization capabilities.
• Extended CNV/SV support.

Features

• Fully automated pipeline for Target Panel Sequencing.
• Supports GATK, Samtools, BWA, ANNOTSV, CNVkit, Control-FREEC, Decon, CNV-z, Panel-cn, CNVPanelizer, and visualization tools.
• Compatible with human genome (hg38/hg19).

Installation

You can install this pipeline using one of the following methods:

1️⃣ Install via Docker

git clone https://github.com/dazauzai/PanelCNV_pipeline.git
cd PanelCNV_pipeline
docker build -t panel_cnv_pipeline .

To run the pipeline with Docker:

docker run --rm -v /path/to/data:/data -v /path/to/output:/output panel_cnv_pipeline \
    -b /data/bam_directory -o /output -r /data/reference_genome \
    -t /data/tumor_sample -d /data/dbsnp_vcf -P /data/pon_file

2️⃣ Install via Git Clone

gh repo clone dazauzai/PanelCNV_pipeline
cd PanelCNV_pipeline

3️⃣ Install via Direct Download

wget https://github.com/dazauzai/PanelCNV_pipeline/archive/main.zip
unzip main.zip
cd PanelCNV_pipeline

Usage

Run the pipeline using the following command:

bash main.sh -b <bam_directory> -o <output_dir> -r <reference_genome> \
             -t <tumor_sample> -d <dbsnp_vcf> -P <panel_pon_file>

Parameters

Parameter	Description	Required
-b	Input directory containing BAM files	✅ Required
-o	Output directory for results	✅ Required
-r	Reference genome file (e.g., hg38.fa)	✅ Required
-t	Tumor sample BAM file	✅ Required
-d	Known SNP database (e.g., dbSNP VCF), required for Control-FREEC if not using hg38	Optional
-P	PON file for CNVkit, used as a reference file for CNV calling	Optional

Output Files

Output varies by tool but generally includes BED files for CNV results and additional variant information.

Future Improvements

• Adding support for CNV and SV detection.
• Improved visualization with interactive reports.
• Expansion to non-human genomes. Acknowledgments

We sincerely thank the developers of the following tools that make this pipeline possible:

CNVkit

Control-FREEC

DECoN

PanelCN

CNV-Z

CNVPanelizer

Samtools

BEDTools

AnnotateSV

GATK

BWA

License

This pipeline is open-source under the MIT License.

Contact

For questions, please contact dazauzai.