RTG Tools
The industry standard for variant comparison and benchmarking.
RTG Tools is a powerful subset of our RTG Core analysis suite, providing a collection of mature, well-tested utilities for processing common NGS data formats. Available for free under the permissive BSD open-source license, RTG Tools encourages the wider adoption of best-practice methods for variant benchmarking.
These utilities represent the same robust, battle-tested software components we use internally and deploy for our clients when building custom bioinformatics pipelines and services.
Technical Highlights
Built on over a decade of algorithmic innovation, RTG Core includes advanced features that set it apart:
- Haplotype-Aware Variant Comparison: vcfeval performs sophisticated variant comparison at the haplotype level, easily handling complex variants and representational differences that confound conventional normalization tools.
- Interactive ROC Analysis: Includes
rocplot, an interactive tool for exploring and visualizing ROC curves from one or morevcfevalruns, aiding in the selection of optimal scoring attributes and filtering thresholds. - Comprehensive VCF Utilities: Powerful commands for VCF filtering, merging, annotation, and Mendelian consistency analysis.
- Format Manipulation: Easily process and convert FASTA/FASTQ, SAM/BAM, BED, and PED formats.
- Simulation Toolkit: A suite of NGS simulation tools to generate synthetic reads and datasets for pipeline development and testing.
About vcfeval
Over the years, one of the most critical challenges in genomics has been accurately comparing genotypes from multiple VCFs. Naive tools that compare variant positions or alleles directly often fail to account for the multiple ways complex variants can be represented.
vcfeval solves this by evaluating variants at the haplotype level—determining whether the genotypes asserted in the VCFs result in the same genomic sequence when applied to the reference genome. To date, no other tool is capable of performing this analysis as accurately and quickly as vcfeval. It has become an essential benchmarking standard, heavily utilized in collaborations with initiatives like the Genome in a Bottle consortium and precisionFDA.
Source Code & Downloads
Documentation
Need help integrating RTG Tools into your workflow? We offer professional Custom Genomic Solutions and Services including pipeline integration, web portal development, and proprietary algorithm design. Contact us to discuss your project.