gbcms¶

Get Base Counts Multi-Sample — High-performance variant counting from BAM files

What It Does¶

GBCMS extracts allele counts and variant metrics at specified positions in BAM files:

flowchart LR
    subgraph Input
        VCF[VCF/MAF]
        BAM[BAM Files]
    end

    subgraph Output
        Counts[Allele Counts]
        Metrics[VAF, Strand Bias]
    end

    VCF --> Engine[gbcms]
    BAM --> Engine
    Engine --> Counts
    Engine --> Metrics

Use mouse to pan and zoom

Visual Overview¶

gbcms overview poster — gbcms end-to-end pipeline — click to enlarge

Detailed Overview (PDF)¶

Key Metrics¶

Metric	Formula	Description
VAF	`AD / (RD + AD)`	Variant Allele Frequency
Strand Bias	Fisher's exact test	Detect sequencing artifacts
Fragment Counts	Deduplicated pairs	PCR-aware counting

Quick Start¶

# Install
pip install gbcms

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

→ Full Installation Guide | → CLI Examples

Choose Your Workflow¶

flowchart TD
    Start[How many samples?] --> Few{1-10 samples}
    Start --> Many{10+ samples}

    Few --> CLI([Use CLI]):::cli
    Many --> HPC{HPC cluster?}

    HPC --> |Yes| Nextflow([Use Nextflow]):::nf
    HPC --> |No| CLI

    classDef cli fill:#4caf50,color:white,stroke:#388e3c,stroke-width:2px;
    classDef nf fill:#2196f3,color:white,stroke:#1565c0,stroke-width:2px;

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Workflow	Best For	Guide
CLI	1-10 samples, local/single server	Quick Start
Nextflow	10+ samples, HPC/SLURM	Nextflow Guide

Architecture¶

Python/Rust hybrid for maximum performance:

flowchart TB
    subgraph Python [🐍 Python]
        CLI[CLI] --> Pipeline[Orchestration]
        Pipeline --> IO[VCF/MAF I/O]
    end

    subgraph Rust [🦀 Rust]
        Counter[BAM Counting]
        Stats[Fisher Test]
    end

    Pipeline --> Counter
    Counter --> Stats

    classDef pythonStyle fill:#3776ab,color:#fff,stroke:#2c5f8a,stroke-width:2px;
    classDef rustStyle fill:#dea584,color:#000,stroke:#c48a6a,stroke-width:2px;
    class Python pythonStyle;
    class Rust rustStyle;

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→ Technical Details | → How It Works

Documentation¶

Section	Description
Getting Started	Installation and first run
CLI Reference	Command-line usage
Nextflow Pipeline	HPC workflow
How It Works	Architecture, algorithms, and formats
Development	Contributing guide