py-gbcms 2.8.0

Python implementation of GetBaseCountsMultiSample (gbcms) for calculating base counts in BAM files

py-gbcms

Complete orientation-aware counting system for genomic variants

Features

• 🚀 High Performance: Rust-powered core engine with multi-threading
• 🧬 Complete Variant Support: SNP, MNP, insertion, deletion, and complex variants (DelIns, SNP+Indel)
• 📊 Orientation-Aware: Forward and reverse strand analysis with fragment counting
• 🔬 Statistical Analysis: Fisher's exact test for strand bias
• 📁 Flexible I/O: VCF and MAF input/output formats
• 🎯 Quality Filters: 8 configurable read and quality filtering options

Installation

Quick install:

pip install py-gbcms

From source (requires Rust):

git clone https://github.com/msk-access/py-gbcms.git
cd py-gbcms
pip install .

Docker:

docker pull ghcr.io/msk-access/py-gbcms:X.Y.Z  # Replace X.Y.Z with latest from PyPI

💡 Find the latest version on PyPI or GHCR.

📖 Full documentation: https://msk-access.github.io/py-gbcms/

---

Usage

py-gbcms can be used in two ways:

🔧 Option 1: Standalone CLI (1-10 samples)

Best for: Quick analysis, local processing, direct control

gbcms run \
    --variants variants.vcf \
    --bam sample1.bam \
    --fasta reference.fa \
    --output-dir results/

Output: results/sample1.vcf

Learn more:

• 📘 CLI Quick Start
• 📖 CLI Reference

---

🔄 Option 2: Nextflow Workflow (10+ samples, HPC)

Best for: Many samples, HPC clusters (SLURM), reproducible pipelines

nextflow run nextflow/main.nf \
    --input samplesheet.csv \
    --variants variants.vcf \
    --fasta reference.fa \
    -profile slurm

Features:

• ✅ Automatic parallelization across samples
• ✅ SLURM/HPC integration
• ✅ Container support (Docker/Singularity)
• ✅ Resume failed runs

Learn more:

• 🔄 Nextflow Workflow Guide
• 📋 Usage Patterns Comparison

---

Which Should I Use?

Scenario	Recommendation
1-10 samples, local machine	CLI
10+ samples, HPC cluster	Nextflow
Quick ad-hoc analysis	CLI
Production pipeline	Nextflow
Need auto-parallelization	Nextflow
Full manual control	CLI

---

Quick Examples

CLI: Single Sample

gbcms run \
    --variants variants.vcf \
    --bam tumor.bam \
    --fasta hg19.fa \
    --output-dir results/ \
    --threads 4

CLI: Multiple Samples (Sequential)

gbcms run \
    --variants variants.vcf \
    --bam-list samples.txt \
    --fasta hg19.fa \
    --output-dir results/

Nextflow: Many Samples (Parallel)

# samplesheet.csv:
# sample,bam,bai
# tumor1,/path/to/tumor1.bam,
# tumor2,/path/to/tumor2.bam,

nextflow run nextflow/main.nf \
    --input samplesheet.csv \
    --variants variants.vcf \
    --fasta hg19.fa \
    --outdir results \
    -profile slurm

---

Documentation

📚 Full Documentation: https://msk-access.github.io/py-gbcms/

Quick Links:

• Installation
• CLI Quick Start
• Nextflow Workflow
• CLI Reference
• Input & Output Formats
• Architecture

---

Contributing

See CONTRIBUTING.md for development guidelines.

To contribute to documentation, see the gh-pages branch.

---

Citation

If you use py-gbcms in your research, please cite:

[Citation to be added]

---

License

AGPL-3.0 - see LICENSE for details.

---

Support

• 🐛 Issues: https://github.com/msk-access/py-gbcms/issues
• 💬 Discussions: https://github.com/msk-access/py-gbcms/discussions