{"id":44278131,"url":"https://github.com/msk-access/py-gbcms","last_synced_at":"2026-02-24T06:00:01.979Z","repository":{"id":326100750,"uuid":"1068141861","full_name":"msk-access/py-gbcms","owner":"msk-access","description":" high-performance tool for extracting base counts and variant metrics from BAM 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3.10+](https://img.shields.io/badge/python-3.10+-blue.svg)](https://www.python.org/downloads/)\n\n## Features\n\n- 🚀 **High Performance**: Rust-powered core engine with multi-threading\n- 🧬 **Complete Variant Support**: SNP, MNP, insertion, deletion, and complex variants (DelIns, SNP+Indel)\n- 📊 **Orientation-Aware**: Forward and reverse strand analysis with fragment counting\n- 🔬 **Statistical Analysis**: Fisher's exact test for strand bias\n- 📁 **Flexible I/O**: VCF and MAF input/output formats\n- 🎯 **Quality Filters**: 7 configurable read filtering options\n\n## Installation\n\n**Quick install:**\n```bash\npip install py-gbcms\n```\n\n**From source (requires Rust):**\n```bash\ngit clone https://github.com/msk-access/py-gbcms.git\ncd py-gbcms\npip install .\n```\n\n**Docker:**\n```bash\ndocker pull ghcr.io/msk-access/py-gbcms:2.1.0\n```\n\n📖 **Full documentation:** https://msk-access.github.io/py-gbcms/\n\n---\n\n## Usage\n\n`py-gbcms` can be used in two ways:\n\n### 🔧 Option 1: Standalone CLI (1-10 samples)\n\n**Best for:** Quick analysis, local processing, direct control\n\n```bash\ngbcms run \\\n    --variants variants.vcf \\\n    --bam sample1.bam \\\n    --fasta reference.fa \\\n    --output-dir results/\n```\n\n**Output:** `results/sample1.vcf`\n\n**Learn more:**\n- 📘 [CLI Quick Start](https://cmo-ci.gitbook.io/py-gbcms/quick-start)\n- 📖 [CLI Reference](https://cmo-ci.gitbook.io/py-gbcms/cli_features)\n\n---\n\n### 🔄 Option 2: Nextflow Workflow (10+ samples, HPC)\n\n**Best for:** Many samples, HPC clusters (SLURM), reproducible pipelines\n\n```bash\nnextflow run nextflow/main.nf \\\n    --input samplesheet.csv \\\n    --variants variants.vcf \\\n    --fasta reference.fa \\\n    -profile slurm\n```\n\n**Features:**\n- ✅ Automatic parallelization across samples\n- ✅ SLURM/HPC integration\n- ✅ Container support (Docker/Singularity)\n- ✅ Resume failed runs\n\n**Learn more:**\n- 🔄 [Nextflow Workflow Guide](https://cmo-ci.gitbook.io/py-gbcms/nextflow)\n- 📋 [Usage Patterns Comparison](https://cmo-ci.gitbook.io/py-gbcms/workflows)\n\n---\n\n## Which Should I Use?\n\n| Scenario | Recommendation |\n|----------|----------------|\n| 1-10 samples, local machine | **CLI** |\n| 10+ samples, HPC cluster | **Nextflow** |\n| Quick ad-hoc analysis | **CLI** |\n| Production pipeline | **Nextflow** |\n| Need auto-parallelization | **Nextflow** |\n| Full manual control | **CLI** |\n\n---\n\n## Quick Examples\n\n### CLI: Single Sample\n```bash\ngbcms run \\\n    --variants variants.vcf \\\n    --bam tumor.bam \\\n    --fasta hg19.fa \\\n    --output-dir results/ \\\n    --threads 4\n```\n\n### CLI: Multiple Samples (Sequential)\n```bash\ngbcms run \\\n    --variants variants.vcf \\\n    --bam-list samples.txt \\\n    --fasta hg19.fa \\\n    --output-dir results/\n```\n\n### Nextflow: Many Samples (Parallel)\n```bash\n# samplesheet.csv:\n# sample,bam,bai\n# tumor1,/path/to/tumor1.bam,\n# tumor2,/path/to/tumor2.bam,\n\nnextflow run nextflow/main.nf \\\n    --input samplesheet.csv \\\n    --variants variants.vcf \\\n    --fasta hg19.fa \\\n    --outdir results \\\n    -profile slurm\n```\n\n---\n\n## Documentation\n\n📚 **Full Documentation:** https://cmo-ci.gitbook.io/py-gbcms/\n\n**Quick Links:**\n- [Installation](https://cmo-ci.gitbook.io/py-gbcms/installation)\n- [CLI Quick Start](https://cmo-ci.gitbook.io/py-gbcms/quick-start)\n- [Nextflow Workflow](https://cmo-ci.gitbook.io/py-gbcms/nextflow)\n- [CLI Reference](https://cmo-ci.gitbook.io/py-gbcms/cli_features)\n- [Input \u0026 Output Formats](https://cmo-ci.gitbook.io/py-gbcms/input_output)\n- [Architecture](https://cmo-ci.gitbook.io/py-gbcms/architecture)\n\n---\n\n## Contributing\n\nSee [CONTRIBUTING.md](CONTRIBUTING.md) for development guidelines.\n\nTo contribute to documentation, see the [`gh-pages` branch](https://github.com/msk-access/py-gbcms/tree/gh-pages).\n\n---\n\n## Citation\n\nIf you use `py-gbcms` in your research, please cite:\n\n```\n[Citation to be added]\n```\n\n---\n\n## License\n\nAGPL-3.0 - see [LICENSE](LICENSE) for details.\n\n---\n\n## Support\n\n- 🐛 **Issues:** https://github.com/msk-access/py-gbcms/issues\n- 💬 **Discussions:** https://github.com/msk-access/py-gbcms/discussions\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmsk-access%2Fpy-gbcms","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fmsk-access%2Fpy-gbcms","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmsk-access%2Fpy-gbcms/lists"}