Running Freebayes with Docker

This README provides instructions on how to run Freebayes, a genetic variant calling program, using Docker. Freebayes can be easily executed within a Docker container, ensuring a consistent and reproducible environment.

Prerequisites

Before getting started, ensure that you have Docker installed on your system. You can download and install Docker from Docker's official website.

Running Freebayes

Replace <version> with the desired version of Freebayes. Version 1.3.7 is recommended

To run Freebayes using Docker, follow these steps:

1. Create a directory Move your fasta file to the ref directory and your Bam file to the bam directory.

2. Run Freebayes Run Freebayes using docker compose up and docker compose run.

3. Create VCF file Execute freebayes -f ref/reference.fa bam/input.bam > var.vcf.

Notes

• Ensure that the paths to your input files (reference.fasta and input.bam) are correct and exist in the mounted directory.
• You can adjust the Docker run command to include additional Freebayes options as needed.

Troubleshooting

If you encounter any issues, verify the following:

• Docker is correctly installed and running on your system.
• The specified paths are correct and accessible.
• Check the Freebayes documentation for any specific command-line arguments that may need adjustment.

Additional Resources

• Freebayes Documentation
• Docker Documentation
• Biocontainers on Docker Hub

By using Docker, you can simplify the deployment and execution of Freebayes, ensuring a consistent computational environment for your genomic analyses.