Update README.md

README.md

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-# freebayes-docker
+# 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](https://www.docker.com/products/docker-desktop).
+
+
+## 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](https://github.com/ekg/freebayes)
+- [Docker Documentation](https://docs.docker.com/)
+- [Biocontainers on Docker Hub](https://quay.io/repository/biocontainers/freebayes)
+
+By using Docker, you can simplify the deployment and execution of Freebayes, ensuring a consistent computational environment for your genomic analyses.
+