Improved simulation tools / Java 11 compatibility
February 26th, 2020
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 several new features and commands, along with the usual assortment of minor features and bug fixes. Several of these result in command line arguments or changes to program outputs, so check existing scripts for compatibility before upgrading. Larger features of note:
- A new command, mapp, for mapping protein query sequences against a protein database. This command is complementary to the existing translated protein search of the mapx command, and usage is very similar.
- A new command for variant calling tumor samples when no matched normal is available. This command, tumoronly, uses a similar bayesian model as the existing somatic command (and several of the improvements made during development of the tumor-only calling scenario have also been applied to the somatic caller). See the user manual for more information.
- Several improvements to simulation tools, particularly oriented toward the simulation of variants within members of a pedigree. Quite substantial improvements to speed and memory use have been made, as well as adding the ability to utilize genetic map files to choose recombination sites when simulating children.