Nanopore Variant Calling

This repository contains a script for performing variant calling using Nanopore sequencing data.

Prerequisites

Before running the script, make sure you have the following software installed:

• NanoPlot
• Minimap2
• Samtools
• Longshot
• Sniffles

Usage

To run the variant calling script, follow these steps:

1. Clone the repository:

   git clone https://github.com/your-username/nanopore_variant_calling.git

2. Navigate to the repository directory:

   cd nanopore_variant_calling/pipeline

3. Run the script:

   ./nanopore_variant_calling.sh 

   It will print the usage:

   Usage: ./nanopore_variant_calling.sh <FASTQ_FILE> <REF_FILE> <OUTPUT_DIR>
   FASTQ_FILE: Path to the input FASTQ file
   REF_FILE: Path to the reference genome file
   OUTPUT_DIR: Directory where the output will be saved

Output

The script will generate the following output files:

• NanoPlot/: Directory containing the output of NanoPlot, which includes various plots and statistics about the quality of the sequencing data.
• aligned.sam: SAM file containing the aligned reads.
• aligned_sorted.bam: BAM file containing the sorted and indexed aligned reads.
• aligned_sorted.bam.bai: Index file for the aligned_sorted.bam file.
• variants.vcf: VCF file containing the detected small variants.
• structural_variants.vcf: VCF file containing the detected structural variants.

Contributing

Contributions are welcome! If you find any issues or have suggestions for improvements, please open an issue or submit a pull request.

License

This project is licensed under the MIT License.