Introduction

gbcms (Get Base Counts Multi-Sample) is a high-performance tool for extracting base counts and variant metrics from BAM files.

Key Features

• Rust-Powered Engine: Maximum performance and memory efficiency

• Accurate Variant Handling: Full VCF/MAF support with rigorous normalization

• Comprehensive Metrics: Depth, strand counts, fragment counts, VAF, and Fisher's strand bias

• Modern CLI: User-friendly interface with rich output

• Flexible Deployment: Standalone CLI or Nextflow workflow

Two Ways to Use gbcms

🔧 Standalone CLI

For processing 1-10 samples locally or on a single server.

gbcms run --variants variants.vcf --bam sample.bam --fasta ref.fa --output-dir results/

→ CLI Quick Start

🔄 Nextflow Workflow

For processing 10+ samples in parallel on HPC clusters.

nextflow run nextflow/main.nf --input samples.csv --variants variants.vcf --fasta ref.fa -profile slurm

→ Nextflow Workflow Guide

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Architecture

gbcms uses a hybrid Python/Rust architecture:

• Python: CLI, input parsing (VCF/MAF), orchestration, and output formatting

• Rust: Computationally intensive read iteration, base pileup, and statistics

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Next Steps

Choose your path:

New to gbcms?

1. Usage Overview - Choose CLI or Nextflow

2. CLI Quick Start OR Nextflow Guide

Contributing:

• Contributing Guide