vcf-reformatter - 🚀 VCF Reformatter v0.3.0 - MAF Support & Memory Optimizations

📊 MAF Output Support (Beta) - New output format: Direct conversion from VCF to Mutation Annotation Format (MAF) - Auto-detection: Automatically extracts sequencing center and sample information from VCF headers - Cancer genomics ready: Standard MAF format compatible with downstream analysis tools

# Generate MAF output
vcf-reformatter sample.vcf.gz --output-format maf

# With custom parameters
vcf-reformatter sample.vcf.gz --output-format maf --center TCGA --sample-barcode TCGA-01

🧠 Memory-Efficient Processing

• Chunked streaming: Large files (>100K variants) now use memory-efficient processing
• Out-of-memory protection: Intelligent warnings for files that may cause memory issues
• Scalable: Handle million+ variant files without memory exhaustion

⚡ Performance Improvements

Feature | Before v0.3.0 | v0.3.0 -- | -- | -- Large files (>100K variants) | Memory bottleneck | Chunked streaming Very large files (>1M variants) | Often failed | Automatic warnings + optimization File I/O | Standard buffering | Streaming output

📦 Installation

# Download pre-compiled binaries (easiest)
wget https://github.com/flalom/vcf-reformatter/releases/download/v0.3.0/vcf-reformatter-v0.3.0-linux-x86_64
chmod +x vcf-reformatter-v0.3.0-linux-x86_64

# Via Conda/Mamba
conda install -c bioconda vcf-reformatter

# Via Cargo
cargo install vcf-reformatter

🔄 Breaking Changes

- None

🐛 Bug Fixes

• Fixed memory issues with very large VCF files
• Improved error messages for malformed input files
• Better handling of edge cases in annotation parsing

🆘 Found an issue? Open a GitHub issue or contact me

🙏 Acknowledgments

Thanks to the community for feedback and feature requests that shaped this release!

⭐ Star this repo if VCF Reformatter helps your research!

- Rust
Published by flalom 10 months ago

vcf-reformatter - 🧬 VCF Reformatter v0.2.0 -SnpEff Support and performance enhancements

Major feature update adding comprehensive SnpEff support and enhanced documentation!

🆕 What's New in v0.2.0

• 🧪 SnpEff ANN Support: Full support for SnpEff ANN annotations alongside existing VEP CSQ
• 🤖 Auto-Detection: Intelligent annotation type detection (VEP/SnpEff/Auto)
• 🛡️ Better Error Handling: More informative error messages and warnings
• 📦 vcf-reformatter in crates.io: Availability also in rust package manager

✨ Key Features

• 🧬 Dual Annotation Support: Parse both VEP (CSQ) and SnpEff (ANN) annotations
• ⚡ High-Performance: 30,000++ variants/sec and parallel processing capabilities
• 🎯 Smart Transcript Handling: Most severe, first only, or split rows strategies
  
• 📊 Analysis-Ready Output: Excel/R/Python-friendly TSV with optional gzip compression
• 🔍 Auto-Detection: Automatically detects annotation type from VCF header
• 🎛️ Flexible CLI: Configurable file names, output paths, threading, and verbosity

📦 Installation

From Crates.io: bash cargo install vcf-reformatter From Binaries: Download from the assets below. From Source: bash git clone https://github.com/flalom/vcf-reformatter.git cd vcf-reformatter cargo build --release

🚀 Usage Examples

```bash

Auto-detect annotation type with verbose output

vcf-reformatter sample.vcf.gz -a auto -v

SnpEff annotations with most severe consequences

vcf-reformatter snpeff_output.vcf.gz -a snpeff -t most-severe -j 4

VEP annotations with compression and custom output

vcf-reformatter vep_output.vcf.gz -a vep -t split -o results/ -c -v

Maximum performance with auto-detection

vcf-reformatter large_cohort.vcf.gz -a auto -t most-severe -j 0 --compress ```

🔄 Breaking Changes

None! v0.2.0 is fully backward compatible with v0.1.0.

🐛 Bug Fixes & Improvements

• Fixed regex dependency constraints for crates.io publication
• Improved header parsing for various VCF formats
• Enhanced error messages for malformed VCF files
• Better handling of edge cases in annotation parsing
• Optimized memory usage for large files

Full Changelog: https://github.com/flalom/vcf-reformatter/compare/v0.1.0...v0.2.0

Thanks to all contributors and users providing feedback! 🙏

- Rust
Published by flalom 11 months ago

vcf-reformatter - VCF Reformatter v0.1.0 - Initial Release

🎉 VCF Reformatter v0.1.0 - Initial Release!

First stable release of VCF Reformatter, a high-performance Rust tool for converting complex VCF files to analyzable and glanceable TSV format.

✨ Key Features

• 🧬 Intelligent VEP annotation parsing with smart transcript handling
• ⚡ High-performance parallel processing (30,000+ variants/sec)
• 🎯 Three transcript strategies: most severe, first only, or split rows
• 📊 Excel/R/Python-ready TSV output with optional gzip compression (⚠️ beware Excel auto-correction!)
• 🔧 User-friendly CLI with error handling

📦 Installation

From Binaries: Download the appropriate binary for your platform from below.

From Source (see also README.md): bash git clone https://github.com/flalom/vcf-reformatter.git cd vcf-reformatter cargo build --release

🚀 Quick Start

``` bash

Basic usage

./vcf-reformatter sample.vcf.gz

High-performance with most severe consequences

./vcf-reformatter large_cohort.vcf.gz -t most-severe -j 0 --compress ```

- Rust
Published by flalom 11 months ago