GenomePhone VarScan Worker

"Ring ring ring ring, GenomePhone"

Introduction

Variant calling is a process in bioinformatics that identifies differences in a genomic sequence compared to a reference sequence. These differences, or variants, can include single nucleotide polymorphisms (SNPs), insertions, deletions, and others. Variant calling plays a crucial role in understanding the genetic basis of diseases, among other applications.

GenomePhone is a framework for distributed variant calling. This repository, genomephone-worker-varscan, is an implementation of a GenomePhone worker that uses the VarScan variant caller. It is written in Kotlin.

The genomephone-worker-varscan is responsible for processing chunks of genomic data using the VarScan variant caller. It receives messages from a Kafka topic, each containing the ID of a chunk to process. It then retrieves the chunk from a database, processes it using VarScan, and stores the results back in the database.

Getting Started

To get started with genomephone-worker-varscan, you’ll need to have Kotlin 1.9 installed on your machine. Once Kotlin is installed, you can clone this repository and build the project.

Clone the Repository

git clone https://github.com/GenomePhone/genomephone-worker-varscan.git
cd genomephone-worker-varscan

Build the Project

./gradlew build

Usage

After building the project, you can run the application.

./gradlew run

Contributing

We welcome contributions to genomephone-worker-varscan! If you have a feature request, bug report, or proposal, please open an issue on this GitHub repository.

License

genomephone-worker-varscan is licensed under the MIT License. See the LICENSE file for more details.