Somatic calling / CGI v2 reads support / VCF comparison improvements
December 06, 2015
Real Time Genomics are pleased to announce the availability of new releases of our full analysis suite, RTG Core, and our utility package, RTG Tools. This release includes new features and performance improvements. Some of the highlights of this release:
- Further improvements to somatic variant calling which reduce the number of false positive calls while retaining somatic calling sensitivity. These improvements are achieved by incorporating the presence of somatic-allele-supporting evidence in the normal into the Bayesian computation. Additional VCF annotations quantifying these "contrary observations" are included in the output.
- De novo variant detection in families and pedigrees now incorporates similar techniques for a reduction in false positives.
- Support for aligning and variant calling with reads produced by Complete Genomics Inc has been extended to their newer 29 base-pair read structure (these reads consisting of 10-9-10 sub-reads are often represented as 30 base-pairs with a redundant N).
- Many improvements to variant comparison with vcfeval, including the improved handling of call sets containing overlapping variants, identification of variants which do not constitute a diploid match but which share a common allele (e.g. zygosity errors), and the ability to select alternative output modes depending on the desired analysis workflow.
- Many other minor improvements (full release notes are included in the product downloads.)
Special thanks to the members of the GA4GH benchmarking data working group (in particular Justin Zook, Rebecca Truty, Peter Kruche, and Kevin Jacobs) for valuable feedback and suggestions for improvements to vcfeval that are available in this release.
If you haven't used RTG Core before (or maybe even if you have), we suggest you run the demo-family.sh script that runs through a short 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.)