Getting Started

Welcome to py-gbcms! This section will help you get up and running quickly.

What You'll Learn

• Installation — Install via PyPI, Docker, or from source
• Quick Start — Run your first variant counting job

Prerequisites

• Python 3.9+
• BAM file(s) with index (.bai)
• Reference FASTA with index (.fai)
• VCF or MAF file with variant positions

Next Steps

Once installed, try the Quick Start guide to run your first job.

For processing many samples in parallel, see the Nextflow Pipeline.