Somatic calling / metagenomic improvements / RTG Tools BSD Licensed
July 16, 2015
Real Time Genomics are pleased to announce the availability of new releases of our full analysis suite, RTG Core 3.5, and our free utility package, RTG Tools 3.5. This release includes new features and performance improvements. Some of the highlights of this release:
- Several improvements to somatic variant calling, including the ability to specify site-specific somatic priors, control of output for gain-of-reference and loss-of-heterozygosity events, and changes to the VCF to align with TCGA VCF specification.
- Improvements to metagenomic species reference database management. Several new options allow better customization of a species reference, and extraction of genomic information for individual species contained within the reference database.
- Improvements to variant evaluation with vcfeval, primarily the ability to perform evaluation restricted to individual regions or sets of regions (for example GiaB high-confidence intervals or exome target regions), and the inclusion of more accuracy metrics, both as a new summary file and included in the weighted ROC data file.
- We are also pleased to make the source code to RTG Tools available under the Simplified BSD License, on github. (Source code for RTG Core remains available for non-commercial use).
- Many other smaller improvements (full release notes are included in the product downloads).
If you haven't used RTG Core before (or maybe even if you have), it includes a nice new demo script that runs through an end-to-end demonstration of sex-aware and pedigree-aware family variant calling, including de novo variant detection and variant evaluation with vcfeval. (It also makes a nice demo of our comprehensive simulation tools.)